{"gene":"MINDY3","run_date":"2026-04-28T18:30:28","timeline":{"discoveries":[{"year":2016,"finding":"MINDY-family deubiquitinases (founding member MINDY-1/FAM63A, with MINDY3/FAM63B identified as a family member) are highly selective K48-linked polyubiquitin chain cleaving enzymes encoded by a previously unannotated catalytic domain with a distinct protein fold bearing no homology to known DUB families; crystal structure of MINDY-1 in complex with propargylated ubiquitin revealed conformational changes that realign the active site for catalysis, and the enzymes preferentially trim long K48-linked chains from the distal end.","method":"Crystal structure determination, activity-based probe labeling with propargylated ubiquitin, in vitro DUB activity assays with linkage-specific di-ubiquitin substrates, active-site mutagenesis","journal":"Molecular Cell","confidence":"High","confidence_rationale":"Tier 1 — crystal structure plus reconstituted in vitro activity and mutagenesis in a single rigorous study; establishes the MINDY family to which MINDY3 belongs","pmids":["27292798"],"is_preprint":false}],"current_model":"MINDY3 (FAM63B) belongs to the evolutionarily conserved MINDY family of deubiquitinases, defined by a structurally unique catalytic domain that selectively cleaves K48-linked polyubiquitin chains (a degradation signal), trimming chains from the distal end; no experiments directly characterizing MINDY3 itself (as distinct from its paralog MINDY-1/FAM63A) are present in the available literature."},"narrative":{"teleology":[{"year":2016,"claim":"Identification of the MINDY catalytic domain as a novel DUB fold with K48-linkage selectivity established the enzymatic family to which MINDY3 belongs, resolving its previously unannotated catalytic potential.","evidence":"Crystal structure of MINDY-1 with propargylated ubiquitin, in vitro DUB assays with linkage-specific diubiquitin substrates, and active-site mutagenesis","pmids":["27292798"],"confidence":"High","gaps":["All structural and biochemical data derive from the paralog MINDY-1/FAM63A; MINDY3 itself has not been biochemically characterized","No cellular substrates or biological processes have been assigned to MINDY3","No structural model of MINDY3 exists"]},{"year":null,"claim":"Whether MINDY3 shares the same K48-linkage selectivity, chain-length preference, and catalytic efficiency as MINDY-1, and what its endogenous substrates and physiological roles are, remain entirely open questions.","evidence":"","pmids":[],"confidence":"Low","gaps":["No direct enzymatic assay of recombinant MINDY3 has been reported","No loss-of-function or gain-of-function cellular studies for MINDY3 exist","Tissue-specific expression and regulation of MINDY3 are unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0]},{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[0]}],"localization":[],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0]}],"complexes":[],"partners":[],"other_free_text":[]},"mechanistic_narrative":"MINDY3 (FAM63B) is a member of the MINDY family of deubiquitinases, which possess a structurally unique catalytic domain with no homology to other known DUB families and selectively cleave K48-linked polyubiquitin chains, preferentially trimming long chains from the distal end [PMID:27292798]. No experiments directly characterizing MINDY3 itself—as distinct from the founding family member MINDY-1/FAM63A—are present in the available literature; its specific substrates, regulation, and cellular roles remain uncharacterized."},"prefetch_data":{"uniprot":{"accession":"Q9H8M7","full_name":"Ubiquitin carboxyl-terminal hydrolase MINDY-3","aliases":["Dermal papilla-derived protein 5","Deubiquitinating enzyme MINDY-3","Protein CARP"],"length_aa":445,"mass_kda":49.7,"function":"Hydrolase that can remove 'Lys-48'-linked conjugated ubiquitin from proteins","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q9H8M7/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/MINDY3","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/MINDY3","total_profiled":1310},"omim":[{"mim_id":"618408","title":"MINDY LYSINE-48 DEUBIQUITINASE 2; MINDY2","url":"https://www.omim.org/entry/618408"},{"mim_id":"618407","title":"MINDY LYSINE-48 DEUBIQUITINASE 1; MINDY1","url":"https://www.omim.org/entry/618407"},{"mim_id":"611649","title":"MINDY LYSINE-48 DEUBIQUITINASE 3; MINDY3","url":"https://www.omim.org/entry/611649"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Nuclear membrane","reliability":"Supported"},{"location":"Microtubules","reliability":"Additional"},{"location":"Primary cilium","reliability":"Additional"},{"location":"Primary cilium tip","reliability":"Additional"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/MINDY3"},"hgnc":{"alias_symbol":["FLJ13397","CARP","my042","DERP5"],"prev_symbol":["C10orf97","FAM188A"]},"alphafold":{"accession":"Q9H8M7","domains":[{"cath_id":"-","chopping":"1-112_147-195","consensus_level":"medium","plddt":91.2647,"start":1,"end":195},{"cath_id":"1.10.238.10","chopping":"304-368","consensus_level":"high","plddt":92.9777,"start":304,"end":368},{"cath_id":"-","chopping":"377-435","consensus_level":"medium","plddt":91.6039,"start":377,"end":435}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H8M7","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H8M7-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H8M7-F1-predicted_aligned_error_v6.png","plddt_mean":87.81},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=MINDY3","jax_strain_url":"https://www.jax.org/strain/search?query=MINDY3"},"sequence":{"accession":"Q9H8M7","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9H8M7.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9H8M7/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H8M7"}},"corpus_meta":[{"pmid":"12553453","id":"PMC_12553453","title":"Spring viremia of carp (SVC).","date":"2002","source":"Diseases of aquatic organisms","url":"https://pubmed.ncbi.nlm.nih.gov/12553453","citation_count":279,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"25759845","id":"PMC_25759845","title":"Insights into the antiviral immunity against grass carp (Ctenopharyngodon idella) reovirus (GCRV) in grass carp.","date":"2015","source":"Journal of immunology research","url":"https://pubmed.ncbi.nlm.nih.gov/25759845","citation_count":199,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"26905065","id":"PMC_26905065","title":"Spring viraemia of carp virus: recent advances.","date":"2016","source":"The Journal of general virology","url":"https://pubmed.ncbi.nlm.nih.gov/26905065","citation_count":143,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"27514729","id":"PMC_27514729","title":"Environment shapes the fecal microbiome of invasive carp species.","date":"2016","source":"Microbiome","url":"https://pubmed.ncbi.nlm.nih.gov/27514729","citation_count":125,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"23269803","id":"PMC_23269803","title":"Comparative genomics of carp herpesviruses.","date":"2012","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/23269803","citation_count":111,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"32800238","id":"PMC_32800238","title":"Cadmium exposure induces pyroptosis of lymphocytes in carp pronephros and spleens by activating NLRP3.","date":"2020","source":"Ecotoxicology and environmental safety","url":"https://pubmed.ncbi.nlm.nih.gov/32800238","citation_count":103,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"25376386","id":"PMC_25376386","title":"Spring viraemia of carp virus induces autophagy for necessary viral replication.","date":"2014","source":"Cellular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/25376386","citation_count":73,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"11229053","id":"PMC_11229053","title":"Hematology and clinical chemistry of cyprinid fish. Common carp and goldfish.","date":"1999","source":"The veterinary clinics of North America. Exotic animal practice","url":"https://pubmed.ncbi.nlm.nih.gov/11229053","citation_count":68,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"34488159","id":"PMC_34488159","title":"Quercetin antagonizes imidacloprid-induced mitochondrial apoptosis through PTEN/PI3K/AKT in grass carp hepatocytes.","date":"2021","source":"Environmental pollution (Barking, Essex : 1987)","url":"https://pubmed.ncbi.nlm.nih.gov/34488159","citation_count":68,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"22303472","id":"PMC_22303472","title":"Identification and profiling of microRNAs from skeletal muscle of the common carp.","date":"2012","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/22303472","citation_count":65,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"28595568","id":"PMC_28595568","title":"Differences in responses of grass carp to different types of grass carp reovirus (GCRV) and the mechanism of hemorrhage revealed by transcriptome sequencing.","date":"2017","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/28595568","citation_count":63,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"27353086","id":"PMC_27353086","title":"MLP and CARP are linked to chronic PKCα signalling in dilated cardiomyopathy.","date":"2016","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/27353086","citation_count":61,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"16650915","id":"PMC_16650915","title":"DNA vaccination can protect Cyprinus Carpio against spring viraemia of carp virus.","date":"2006","source":"Vaccine","url":"https://pubmed.ncbi.nlm.nih.gov/16650915","citation_count":60,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"10524261","id":"PMC_10524261","title":"Uncoupling protein 2 from carp and zebrafish, ectothermic vertebrates.","date":"1999","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/10524261","citation_count":57,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"31881427","id":"PMC_31881427","title":"Tissue distribution and bioaccumulation of a novel polyfluoroalkyl benzenesulfonate in crucian carp.","date":"2019","source":"Environment international","url":"https://pubmed.ncbi.nlm.nih.gov/31881427","citation_count":56,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"22182503","id":"PMC_22182503","title":"Pro-inflammatory functions of carp CXCL8-like and CXCb chemokines.","date":"2011","source":"Developmental and comparative immunology","url":"https://pubmed.ncbi.nlm.nih.gov/22182503","citation_count":56,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"25655327","id":"PMC_25655327","title":"Identification and characterization of MAVS from black carp Mylopharyngodon piceus.","date":"2015","source":"Fish & shellfish immunology","url":"https://pubmed.ncbi.nlm.nih.gov/25655327","citation_count":55,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"16483138","id":"PMC_16483138","title":"3D reconstruction and capsid protein characterization of grass carp reovirus.","date":"2005","source":"Science in China. Series C, Life sciences","url":"https://pubmed.ncbi.nlm.nih.gov/16483138","citation_count":53,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"12590965","id":"PMC_12590965","title":"CpG oligodeoxynucleotides activate grass carp (Ctenopharyngodon idellus) macrophages.","date":"2003","source":"Developmental and comparative immunology","url":"https://pubmed.ncbi.nlm.nih.gov/12590965","citation_count":52,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"16322508","id":"PMC_16322508","title":"Evidence for recombination of mitochondrial DNA in triploid crucian carp.","date":"2005","source":"Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/16322508","citation_count":49,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"29546544","id":"PMC_29546544","title":"Detection of target DNA with a novel Cas9/sgRNAs-associated reverse PCR (CARP) technique.","date":"2018","source":"Analytical and bioanalytical chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/29546544","citation_count":47,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"16362306","id":"PMC_16362306","title":"HIF-1alpha and iNOS levels in crucian carp gills during hypoxia-induced transformation.","date":"2005","source":"Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology","url":"https://pubmed.ncbi.nlm.nih.gov/16362306","citation_count":47,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"30412895","id":"PMC_30412895","title":"Hepatotoxicity and immunotoxicity of MC-LR on silver carp.","date":"2018","source":"Ecotoxicology and environmental safety","url":"https://pubmed.ncbi.nlm.nih.gov/30412895","citation_count":44,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"31580934","id":"PMC_31580934","title":"Atrazine induces necroptosis by miR-181-5p targeting inflammation and glycometabolism in carp lymphocytes.","date":"2019","source":"Fish & shellfish immunology","url":"https://pubmed.ncbi.nlm.nih.gov/31580934","citation_count":44,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"2753359","id":"PMC_2753359","title":"Carp growth hormone: molecular cloning and sequencing of cDNA.","date":"1989","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/2753359","citation_count":44,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"20885956","id":"PMC_20885956","title":"Trypanosomiasis-induced Th17-like immune responses in carp.","date":"2010","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/20885956","citation_count":43,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"19556550","id":"PMC_19556550","title":"High cGMP synthetic activity in carp cones.","date":"2009","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/19556550","citation_count":42,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"27079451","id":"PMC_27079451","title":"Establishing targeted carp TLR22 gene disruption via homologous recombination using CRISPR/Cas9.","date":"2016","source":"Developmental and comparative immunology","url":"https://pubmed.ncbi.nlm.nih.gov/27079451","citation_count":39,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"164348","id":"PMC_164348","title":"Crystalline adenylate kinase from carp muscle.","date":"1975","source":"European journal of biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/164348","citation_count":39,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"25976542","id":"PMC_25976542","title":"Another potential carp killer?: Carp Edema Virus disease in Germany.","date":"2015","source":"BMC veterinary research","url":"https://pubmed.ncbi.nlm.nih.gov/25976542","citation_count":38,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"25033755","id":"PMC_25033755","title":"Pierisins and CARP-1: ADP-ribosylation of DNA by ARTCs in butterflies and shellfish.","date":"2015","source":"Current topics in microbiology and immunology","url":"https://pubmed.ncbi.nlm.nih.gov/25033755","citation_count":38,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"11453652","id":"PMC_11453652","title":"Identification of a novel human ankyrin-repeated protein homologous to CARP.","date":"2001","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/11453652","citation_count":37,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"23087022","id":"PMC_23087022","title":"Abnormal cerebellar development and ataxia in CARP VIII morphant zebrafish.","date":"2012","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/23087022","citation_count":36,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"2920175","id":"PMC_2920175","title":"Purification of carp growth hormone and cloning of the complementary DNA.","date":"1989","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/2920175","citation_count":36,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"15919732","id":"PMC_15919732","title":"Cell proliferation and gill morphology in anoxic crucian carp.","date":"2005","source":"American journal of physiology. Regulatory, integrative and comparative physiology","url":"https://pubmed.ncbi.nlm.nih.gov/15919732","citation_count":35,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"12034023","id":"PMC_12034023","title":"The immune responses of common carp, Cyprinus carpio L., injected with carp interleukin-1beta gene.","date":"2002","source":"Journal of interferon & cytokine research : the official journal of the International Society for Interferon and Cytokine Research","url":"https://pubmed.ncbi.nlm.nih.gov/12034023","citation_count":35,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"32858329","id":"PMC_32858329","title":"DEHP-induce damage in grass carp hepatocytes and the remedy of Eucalyptol.","date":"2020","source":"Ecotoxicology and environmental safety","url":"https://pubmed.ncbi.nlm.nih.gov/32858329","citation_count":33,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"27062969","id":"PMC_27062969","title":"A role for multiple estrogen receptors in immune regulation of common carp.","date":"2016","source":"Developmental and comparative immunology","url":"https://pubmed.ncbi.nlm.nih.gov/27062969","citation_count":32,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"38167330","id":"PMC_38167330","title":"Deciphering the gut microbiome of grass carp through multi-omics approach.","date":"2024","source":"Microbiome","url":"https://pubmed.ncbi.nlm.nih.gov/38167330","citation_count":31,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"20640908","id":"PMC_20640908","title":"Characterization of the nonstructural protein NS80 of grass carp reovirus.","date":"2010","source":"Archives of virology","url":"https://pubmed.ncbi.nlm.nih.gov/20640908","citation_count":31,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"18076744","id":"PMC_18076744","title":"Clonal diversity and genealogical relationships of gibel carp in four hatcheries.","date":"2007","source":"Animal genetics","url":"https://pubmed.ncbi.nlm.nih.gov/18076744","citation_count":31,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"24819892","id":"PMC_24819892","title":"Identification and characterization of microRNAs in the spleen of common carp immune organ.","date":"2014","source":"Journal of cellular biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/24819892","citation_count":30,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"30300738","id":"PMC_30300738","title":"Oral delivery of Bacillus subtilis spores expressing grass carp reovirus VP4 protein produces protection against grass carp reovirus infection.","date":"2018","source":"Fish & shellfish immunology","url":"https://pubmed.ncbi.nlm.nih.gov/30300738","citation_count":30,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"20852740","id":"PMC_20852740","title":"The LIM Protein Zyxin Binds CARP-1 and Promotes Apoptosis.","date":"2010","source":"Genes & cancer","url":"https://pubmed.ncbi.nlm.nih.gov/20852740","citation_count":29,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"25483372","id":"PMC_25483372","title":"Atrazine and chlorpyrifos exposure induces liver autophagic response in common carp.","date":"2014","source":"Ecotoxicology and environmental safety","url":"https://pubmed.ncbi.nlm.nih.gov/25483372","citation_count":29,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"35564045","id":"PMC_35564045","title":"Asian Carp, an Alternative Material for Surimi Production: Progress and Future.","date":"2022","source":"Foods (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/35564045","citation_count":28,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"22559058","id":"PMC_22559058","title":"Characterization of grass carp reovirus minor core protein VP4.","date":"2012","source":"Virology journal","url":"https://pubmed.ncbi.nlm.nih.gov/22559058","citation_count":27,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"26497092","id":"PMC_26497092","title":"The protective immunity against grass carp reovirus in grass carp induced by a DNA vaccination using single-walled carbon nanotubes as delivery vehicles.","date":"2015","source":"Fish & shellfish immunology","url":"https://pubmed.ncbi.nlm.nih.gov/26497092","citation_count":27,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"30925159","id":"PMC_30925159","title":"Spring viraemia of carp virus modulates p53 expression using two distinct mechanisms.","date":"2019","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/30925159","citation_count":26,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"24122108","id":"PMC_24122108","title":"Detection of grass carp reovirus (GCRV) with monoclonal antibodies.","date":"2014","source":"Archives of virology","url":"https://pubmed.ncbi.nlm.nih.gov/24122108","citation_count":26,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"28526571","id":"PMC_28526571","title":"The antiviral signaling mediated by black carp MDA5 is positively regulated by LGP2.","date":"2017","source":"Fish & shellfish immunology","url":"https://pubmed.ncbi.nlm.nih.gov/28526571","citation_count":26,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"27173223","id":"PMC_27173223","title":"Characterization of grass carp spleen transcriptome during GCRV infection.","date":"2016","source":"Genetics and molecular research : GMR","url":"https://pubmed.ncbi.nlm.nih.gov/27173223","citation_count":25,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"29408645","id":"PMC_29408645","title":"Novel subunit vaccine based on grass carp reovirus VP35 protein provides protective immunity against grass carp hemorrhagic disease.","date":"2018","source":"Fish & shellfish immunology","url":"https://pubmed.ncbi.nlm.nih.gov/29408645","citation_count":25,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"21547066","id":"PMC_21547066","title":"Massive production of all-female diploids and triploids in the crucian carp.","date":"2011","source":"International journal of biological sciences","url":"https://pubmed.ncbi.nlm.nih.gov/21547066","citation_count":23,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"23930591","id":"PMC_23930591","title":"Characterization and expression analysis of common carp Cyprinus carpio TLR5M.","date":"2013","source":"DNA and cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/23930591","citation_count":23,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"24316377","id":"PMC_24316377","title":"Elevated expression of Piwi and piRNAs in ovaries of triploid crucian carp.","date":"2013","source":"Molecular and cellular endocrinology","url":"https://pubmed.ncbi.nlm.nih.gov/24316377","citation_count":23,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"23791859","id":"PMC_23791859","title":"Characterization of MMP-9 gene from grass carp (Ctenopharyngodon idella): an Aeromonas hydrophila-inducible factor in grass carp immune system.","date":"2013","source":"Fish & shellfish immunology","url":"https://pubmed.ncbi.nlm.nih.gov/23791859","citation_count":23,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"27999090","id":"PMC_27999090","title":"Biologically active recombinant carp LH as a spawning-inducing agent for carp.","date":"2016","source":"The Journal of endocrinology","url":"https://pubmed.ncbi.nlm.nih.gov/27999090","citation_count":22,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"8829807","id":"PMC_8829807","title":"Purification and molecular cloning of carp ovarian cystatin.","date":"1996","source":"Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/8829807","citation_count":22,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"31015064","id":"PMC_31015064","title":"A developed subunit vaccine based on fiber protein VP56 of grass carp reovirus providing immune protection against grass carp hemorrhagic disease.","date":"2019","source":"Fish & shellfish immunology","url":"https://pubmed.ncbi.nlm.nih.gov/31015064","citation_count":22,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"29017940","id":"PMC_29017940","title":"Single-walled carbon nanotubes as delivery vehicles enhance the immunoprotective effect of a DNA vaccine against spring viremia of carp virus in common carp.","date":"2017","source":"Fish & shellfish immunology","url":"https://pubmed.ncbi.nlm.nih.gov/29017940","citation_count":22,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"22361281","id":"PMC_22361281","title":"Genomic organization, promoter activity of grass carp MDA5 and the association of its polymorphisms with susceptibility/resistance to grass carp reovirus.","date":"2012","source":"Molecular immunology","url":"https://pubmed.ncbi.nlm.nih.gov/22361281","citation_count":21,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"23045532","id":"PMC_23045532","title":"Low activation and fast inactivation of transducin in carp cones.","date":"2012","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/23045532","citation_count":20,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"21967867","id":"PMC_21967867","title":"Genomic structure of grass carp Mx2 and the association of its polymorphisms with susceptibility/resistance to grass carp reovirus.","date":"2011","source":"Molecular immunology","url":"https://pubmed.ncbi.nlm.nih.gov/21967867","citation_count":20,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"31580936","id":"PMC_31580936","title":"Preliminary screening and immunogenicity analysis of antigenic epitopes of spring viremia of carp virus.","date":"2019","source":"Fish & shellfish immunology","url":"https://pubmed.ncbi.nlm.nih.gov/31580936","citation_count":19,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"37281650","id":"PMC_37281650","title":"Ultrastructure and Ultracytochemistry of Fertilization Envelope Formation in the Carp Egg: (vitelline envelope/fertilization envelope/ultrastructure/ultracytochemistry/carp egg).","date":"1982","source":"Development, growth & differentiation","url":"https://pubmed.ncbi.nlm.nih.gov/37281650","citation_count":18,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"22650435","id":"PMC_22650435","title":"Molecular identification of hybrids of the invasive gibel carp Carassius auratus gibelio and crucian carp Carassius carassius in Swedish waters.","date":"2012","source":"Journal of fish biology","url":"https://pubmed.ncbi.nlm.nih.gov/22650435","citation_count":18,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"33591327","id":"PMC_33591327","title":"Uniparental Genome Elimination in Australian Carp Gudgeons.","date":"2021","source":"Genome biology and evolution","url":"https://pubmed.ncbi.nlm.nih.gov/33591327","citation_count":18,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"12506399","id":"PMC_12506399","title":"Cyclin A2 is differentially expressed during oocyte maturation between gynogenetic silver crucian carp and gonochoristic color crucian carp.","date":"2003","source":"Journal of experimental zoology. Part A, Comparative experimental biology","url":"https://pubmed.ncbi.nlm.nih.gov/12506399","citation_count":18,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"31465876","id":"PMC_31465876","title":"Effects of stress and cortisol on the polarization of carp macrophages.","date":"2019","source":"Fish & shellfish immunology","url":"https://pubmed.ncbi.nlm.nih.gov/31465876","citation_count":17,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"35386717","id":"PMC_35386717","title":"Fructose Promotes Crucian Carp Survival Against Aeromonas hydrophila Infection.","date":"2022","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/35386717","citation_count":17,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"26332502","id":"PMC_26332502","title":"Molecular cloning and characterization of IKKε gene from black carp Mylopharyngodon piceus.","date":"2015","source":"Fish & shellfish immunology","url":"https://pubmed.ncbi.nlm.nih.gov/26332502","citation_count":17,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"24287371","id":"PMC_24287371","title":"Immune gene discovery in the crucian carp Carassius auratus.","date":"2013","source":"Fish & shellfish immunology","url":"https://pubmed.ncbi.nlm.nih.gov/24287371","citation_count":17,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"21377537","id":"PMC_21377537","title":"Cloning and characterization of TIMP-2b gene in grass carp.","date":"2011","source":"Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/21377537","citation_count":17,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"26766176","id":"PMC_26766176","title":"Recombinant carp IL-4/13B stimulates in vitro proliferation of carp IgM(+) B cells.","date":"2016","source":"Fish & shellfish immunology","url":"https://pubmed.ncbi.nlm.nih.gov/26766176","citation_count":17,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"27590028","id":"PMC_27590028","title":"Spring viraemia of carp virus enters grass carp ovary cells via clathrin-mediated endocytosis and macropinocytosis.","date":"2016","source":"The Journal of general virology","url":"https://pubmed.ncbi.nlm.nih.gov/27590028","citation_count":16,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"34269137","id":"PMC_34269137","title":"Koi sleepy disease as a pathophysiological and immunological consequence of a branchial infection of common carp with carp edema virus.","date":"2021","source":"Virulence","url":"https://pubmed.ncbi.nlm.nih.gov/34269137","citation_count":16,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"11074593","id":"PMC_11074593","title":"Environmental acclimatization of the carp modulates the transcription of beta-actin.","date":"2000","source":"Journal of cellular biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/11074593","citation_count":16,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"36030005","id":"PMC_36030005","title":"Hepatopancreas toxicity and immunotoxicity of a fungicide, pyraclostrobin, on common carp.","date":"2022","source":"Comparative biochemistry and physiology. Toxicology & pharmacology : CBP","url":"https://pubmed.ncbi.nlm.nih.gov/36030005","citation_count":15,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"17939124","id":"PMC_17939124","title":"Developmental expression of CagMdkb during gibel carp embryogenesis.","date":"2007","source":"The International journal of developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/17939124","citation_count":14,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"30890433","id":"PMC_30890433","title":"Characterisation and function of TRIM23 in grass carp (Ctenopharyngodon idella).","date":"2019","source":"Fish & shellfish immunology","url":"https://pubmed.ncbi.nlm.nih.gov/30890433","citation_count":13,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"18334952","id":"PMC_18334952","title":"Identification of differentially expressed genes in carp rods and cones.","date":"2008","source":"Molecular vision","url":"https://pubmed.ncbi.nlm.nih.gov/18334952","citation_count":13,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"28305738","id":"PMC_28305738","title":"Expression of carp-cdx1, a caudal homolog, in embryos of the carp, Cyprinus carpio.","date":"1995","source":"Roux's archives of developmental biology : the official organ of the EDBO","url":"https://pubmed.ncbi.nlm.nih.gov/28305738","citation_count":13,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"2001405","id":"PMC_2001405","title":"Cloning and characterization of the carp prolactin gene.","date":"1991","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/2001405","citation_count":13,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"28219339","id":"PMC_28219339","title":"Deep Illumina sequencing reveals conserved and novel microRNAs in grass carp in response to grass carp reovirus infection.","date":"2017","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/28219339","citation_count":13,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"1725821","id":"PMC_1725821","title":"Epitopes of the Plasmodium falciparum clustered-asparagine-rich protein (CARP) recognized by human T-cells and antibodies.","date":"1991","source":"Parasite immunology","url":"https://pubmed.ncbi.nlm.nih.gov/1725821","citation_count":12,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"26370541","id":"PMC_26370541","title":"Identification and characterization of IKKε gene from grass carp Ctenopharyngodon idella.","date":"2015","source":"Fish & shellfish immunology","url":"https://pubmed.ncbi.nlm.nih.gov/26370541","citation_count":12,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"30287346","id":"PMC_30287346","title":"Comparative analysis of spleen transcriptome detects differences in evolutionary adaptation of immune defense functions in bighead carp and silver carp.","date":"2018","source":"Fish & shellfish immunology","url":"https://pubmed.ncbi.nlm.nih.gov/30287346","citation_count":12,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"8454022","id":"PMC_8454022","title":"Plasmodium falciparum: the immune response in rabbits to the clustered asparagine-rich protein (CARP) after immunization in Freund's adjuvant or immunostimulating complexes (ISCOMs).","date":"1993","source":"Experimental parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/8454022","citation_count":12,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"34896595","id":"PMC_34896595","title":"Cadmium regulates FKBP5 through miR-9-5p and induces carp lymphocyte apoptosis.","date":"2021","source":"Fish & shellfish immunology","url":"https://pubmed.ncbi.nlm.nih.gov/34896595","citation_count":11,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"30769864","id":"PMC_30769864","title":"A H2AX⁻CARP-1 Interaction Regulates Apoptosis Signaling Following DNA Damage.","date":"2019","source":"Cancers","url":"https://pubmed.ncbi.nlm.nih.gov/30769864","citation_count":11,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"34231974","id":"PMC_34231974","title":"It is everywhere-A survey on the presence of carp edema virus in carp populations in Germany.","date":"2021","source":"Transboundary and emerging diseases","url":"https://pubmed.ncbi.nlm.nih.gov/34231974","citation_count":11,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"29951063","id":"PMC_29951063","title":"Peculiar Expression of CD3-Epsilon in Kidney of Ginbuna Crucian Carp.","date":"2018","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/29951063","citation_count":11,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"31012499","id":"PMC_31012499","title":"Potential vector species of carp edema virus (CEV).","date":"2019","source":"Journal of fish diseases","url":"https://pubmed.ncbi.nlm.nih.gov/31012499","citation_count":11,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"38933191","id":"PMC_38933191","title":"Evolutionary divergence of subgenomes in common carp provides insights into speciation and allopolyploid success.","date":"2023","source":"Fundamental research","url":"https://pubmed.ncbi.nlm.nih.gov/38933191","citation_count":11,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"28232196","id":"PMC_28232196","title":"Molecular cloning of the MARCH family in grass carp (Ctenopharyngodon idellus) and their response to grass carp reovirus challenge.","date":"2017","source":"Fish & shellfish immunology","url":"https://pubmed.ncbi.nlm.nih.gov/28232196","citation_count":11,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"29882019","id":"PMC_29882019","title":"Genome-Scale Association Study of Abnormal Scale Pattern in Yellow River Carp Identified Previously Known Causative Gene in European Mirror Carp.","date":"2018","source":"Marine biotechnology (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/29882019","citation_count":11,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"28550373","id":"PMC_28550373","title":"Black carp vasa identifies embryonic and gonadal germ cells.","date":"2017","source":"Development genes and evolution","url":"https://pubmed.ncbi.nlm.nih.gov/28550373","citation_count":10,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"33065277","id":"PMC_33065277","title":"Role of sox30 in regulating testicular steroidogenesis of common carp.","date":"2020","source":"The Journal of steroid biochemistry and molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/33065277","citation_count":10,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"35634331","id":"PMC_35634331","title":"Recombinant Lactococcus lactis Expressing Grass Carp Reovirus VP6 Induces Mucosal Immunity Against Grass Carp Reovirus Infection.","date":"2022","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/35634331","citation_count":10,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"16169070","id":"PMC_16169070","title":"A human protein-protein interaction network: a resource for annotating the proteome.","date":"2005","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/16169070","citation_count":1704,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"12477932","id":"PMC_12477932","title":"Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.","date":"2002","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/12477932","citation_count":1479,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"26186194","id":"PMC_26186194","title":"The BioPlex Network: A Systematic Exploration of the Human Interactome.","date":"2015","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/26186194","citation_count":1118,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"28514442","id":"PMC_28514442","title":"Architecture of the human interactome defines protein communities and disease networks.","date":"2017","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/28514442","citation_count":1085,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"25416956","id":"PMC_25416956","title":"A proteome-scale map of the human interactome network.","date":"2014","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/25416956","citation_count":977,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"32296183","id":"PMC_32296183","title":"A reference map of the human binary protein interactome.","date":"2020","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/32296183","citation_count":849,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"14702039","id":"PMC_14702039","title":"Complete sequencing and characterization of 21,243 full-length human cDNAs.","date":"2003","source":"Nature genetics","url":"https://pubmed.ncbi.nlm.nih.gov/14702039","citation_count":754,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"33961781","id":"PMC_33961781","title":"Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.","date":"2021","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/33961781","citation_count":705,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"21873635","id":"PMC_21873635","title":"Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.","date":"2011","source":"Briefings in bioinformatics","url":"https://pubmed.ncbi.nlm.nih.gov/21873635","citation_count":656,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"16344560","id":"PMC_16344560","title":"Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes.","date":"2005","source":"Genome research","url":"https://pubmed.ncbi.nlm.nih.gov/16344560","citation_count":409,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"27292798","id":"PMC_27292798","title":"MINDY-1 Is a Member of an Evolutionarily Conserved and Structurally Distinct New Family of Deubiquitinating Enzymes.","date":"2016","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/27292798","citation_count":299,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"17207965","id":"PMC_17207965","title":"hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes.","date":"2007","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/17207965","citation_count":222,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"24823311","id":"PMC_24823311","title":"Genome-wide association study of plasma N6 polyunsaturated fatty acids within the cohorts for heart and aging research in genomic epidemiology consortium.","date":"2014","source":"Circulation. Cardiovascular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/24823311","citation_count":175,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"25544563","id":"PMC_25544563","title":"Global mapping of herpesvirus-host protein complexes reveals a transcription strategy for late genes.","date":"2014","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/25544563","citation_count":173,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"29576527","id":"PMC_29576527","title":"Discovery and Characterization of ZUFSP/ZUP1, a Distinct Deubiquitinase Class Important for Genome Stability.","date":"2018","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/29576527","citation_count":150,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"18461144","id":"PMC_18461144","title":"Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance.","date":"2008","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/18461144","citation_count":148,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"18029348","id":"PMC_18029348","title":"Toward a confocal subcellular atlas of the human proteome.","date":"2007","source":"Molecular & cellular proteomics : MCP","url":"https://pubmed.ncbi.nlm.nih.gov/18029348","citation_count":114,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"34599178","id":"PMC_34599178","title":"Ring finger protein 213 assembles into a sensor for ISGylated proteins with antimicrobial activity.","date":"2021","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/34599178","citation_count":107,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"30561431","id":"PMC_30561431","title":"A protein-protein interaction map of the TNF-induced NF-κB signal transduction pathway.","date":"2018","source":"Scientific data","url":"https://pubmed.ncbi.nlm.nih.gov/30561431","citation_count":74,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"35831314","id":"PMC_35831314","title":"Scalable multiplex co-fractionation/mass spectrometry platform for accelerated protein interactome discovery.","date":"2022","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/35831314","citation_count":65,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"17652099","id":"PMC_17652099","title":"Genome-wide mapping of modifier chromosomal loci for human hypertrophic cardiomyopathy.","date":"2007","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/17652099","citation_count":63,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"31515488","id":"PMC_31515488","title":"Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations.","date":"2019","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/31515488","citation_count":60,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"25260751","id":"PMC_25260751","title":"The MEKK1 PHD ubiquitinates TAB1 to activate MAPKs in response to cytokines.","date":"2014","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/25260751","citation_count":40,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"33277362","id":"PMC_33277362","title":"Global proteomics of Ubqln2-based murine models of ALS.","date":"2020","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/33277362","citation_count":37,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"36168628","id":"PMC_36168628","title":"The N6-methyladenosine-mediated lncRNA WEE2-AS1 promotes glioblastoma progression by stabilizing RPN2.","date":"2022","source":"Theranostics","url":"https://pubmed.ncbi.nlm.nih.gov/36168628","citation_count":32,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"20804422","id":"PMC_20804422","title":"Identification of substrates of SMURF1 ubiquitin ligase activity utilizing protein microarrays.","date":"2010","source":"Assay and drug development technologies","url":"https://pubmed.ncbi.nlm.nih.gov/20804422","citation_count":24,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"38803224","id":"PMC_38803224","title":"K48- and K63-linked ubiquitin chain interactome reveals branch- and length-specific ubiquitin interactors.","date":"2024","source":"Life science alliance","url":"https://pubmed.ncbi.nlm.nih.gov/38803224","citation_count":23,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"12054670","id":"PMC_12054670","title":"CARP is a novel caspase recruitment domain containing pro-apoptotic protein.","date":"2002","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/12054670","citation_count":17,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"24870804","id":"PMC_24870804","title":"CARP is a potential tumor suppressor in gastric carcinoma and a single-nucleotide polymorphism in CARP gene might increase the risk of gastric carcinoma.","date":"2014","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/24870804","citation_count":11,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"21499297","id":"PMC_21499297","title":"C10ORF97 is a novel tumor-suppressor gene of non-small-cell lung cancer and a functional variant of this gene increases the risk of non-small-cell lung cancer.","date":"2011","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/21499297","citation_count":5,"is_preprint":false,"source_track":"gene2pubmed"}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":49365,"output_tokens":34,"usd":0.074302},"stage2":{"model":"","input_tokens":0,"output_tokens":0,"usd":0.0},"total_usd":0.231348,"stage1_batch_id":"msgbatch_01Mgbec4vM6c9vXht7JVJzss","stage2_batch_id":"msgbatch_01JkuuH5RB2BdJNsgnhjbC6s","note":"batch pricing = 50% of standard","round2_stage1":{"model":"claude-sonnet-4-6","input_tokens":62957,"output_tokens":911,"usd":0.101268},"round2_rules_fired":"R1","round2_stage2":{"model":"claude-opus-4-6","input_tokens":3837,"output_tokens":720,"usd":0.055778}},"stage1_raw":"```json\n{\n  \"discoveries\": [],\n  \"current_model\": \"No mechanistic findings in the available literature.\"\n}\n```\n\n--- ROUND 2 (R2/R3, augmented corpus) ---\n\nLooking at the corpus, I need to identify papers actually about MINDY3 (also known as FAM63B, a K48-linked deubiquitinase from the MINDY family).\n\n**Classification:**\n\nThe 100 retrieved papers are overwhelmingly about carp (fish) biology - these are SYMBOL COLLISION/off-target papers with no relevance to human MINDY3. Papers like those about CARP-1/CCAR1 (Cell Cycle and Apoptosis Regulatory Protein), CARP VIII (carbonic anhydrase-related protein), and Plasmodium CARP are all alias collisions with completely different proteins.\n\nFrom the gene2pubmed-curated papers:\n- PMID:27292798 — KEEP: This is directly about the MINDY DUB family discovery, including MINDY-1 (FAM63A). MINDY3 is FAM63B, a paralog in the same family. The paper describes the founding characterization of the MINDY family.\n- PMID:29576527 — KEEP: Discovery of ZUFSP/ZUP1 as a new DUB family; contextually relevant to DUB biology but not specifically about MINDY3.\n- Remaining curated papers: interactome maps (BioPlex, HuRI, Y2H screens) that mention MINDY3 as a detected interactor — these provide protein interaction data but no mechanistic findings specific to MINDY3's function.\n- PMID:28514442, PMID:26186194, PMID:33961781 — BioPlex papers that would list MINDY3 interactions but provide no mechanistic detail about MINDY3 itself.\n\nAfter careful review, PMID:27292798 is the only paper with direct mechanistic relevance to the MINDY family (characterizing MINDY-1/FAM63A as the founding member). No papers in the corpus directly characterize MINDY3 (FAM63B) mechanistically.\n\n```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2016,\n      \"finding\": \"MINDY-family deubiquitinases (founding member MINDY-1/FAM63A, with MINDY3/FAM63B identified as a family member) are highly selective K48-linked polyubiquitin chain cleaving enzymes encoded by a previously unannotated catalytic domain with a distinct protein fold bearing no homology to known DUB families; crystal structure of MINDY-1 in complex with propargylated ubiquitin revealed conformational changes that realign the active site for catalysis, and the enzymes preferentially trim long K48-linked chains from the distal end.\",\n      \"method\": \"Crystal structure determination, activity-based probe labeling with propargylated ubiquitin, in vitro DUB activity assays with linkage-specific di-ubiquitin substrates, active-site mutagenesis\",\n      \"journal\": \"Molecular Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structure plus reconstituted in vitro activity and mutagenesis in a single rigorous study; establishes the MINDY family to which MINDY3 belongs\",\n      \"pmids\": [\"27292798\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"MINDY3 (FAM63B) belongs to the evolutionarily conserved MINDY family of deubiquitinases, defined by a structurally unique catalytic domain that selectively cleaves K48-linked polyubiquitin chains (a degradation signal), trimming chains from the distal end; no experiments directly characterizing MINDY3 itself (as distinct from its paralog MINDY-1/FAM63A) are present in the available literature.\"\n}\n```","stage2_raw":"\n\n--- ROUND 2 (R2/R3, augmented corpus) ---\n\n```json\n{\n  \"mechanistic_narrative\": \"MINDY3 (FAM63B) is a member of the MINDY family of deubiquitinases, which possess a structurally unique catalytic domain with no homology to other known DUB families and selectively cleave K48-linked polyubiquitin chains, preferentially trimming long chains from the distal end [PMID:27292798]. No experiments directly characterizing MINDY3 itself—as distinct from the founding family member MINDY-1/FAM63A—are present in the available literature; its specific substrates, regulation, and cellular roles remain uncharacterized.\",\n  \"teleology\": [\n    {\n      \"year\": 2016,\n      \"claim\": \"Identification of the MINDY catalytic domain as a novel DUB fold with K48-linkage selectivity established the enzymatic family to which MINDY3 belongs, resolving its previously unannotated catalytic potential.\",\n      \"evidence\": \"Crystal structure of MINDY-1 with propargylated ubiquitin, in vitro DUB assays with linkage-specific diubiquitin substrates, and active-site mutagenesis\",\n      \"pmids\": [\"27292798\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"All structural and biochemical data derive from the paralog MINDY-1/FAM63A; MINDY3 itself has not been biochemically characterized\",\n        \"No cellular substrates or biological processes have been assigned to MINDY3\",\n        \"No structural model of MINDY3 exists\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether MINDY3 shares the same K48-linkage selectivity, chain-length preference, and catalytic efficiency as MINDY-1, and what its endogenous substrates and physiological roles are, remain entirely open questions.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No direct enzymatic assay of recombinant MINDY3 has been reported\",\n        \"No loss-of-function or gain-of-function cellular studies for MINDY3 exist\",\n        \"Tissue-specific expression and regulation of MINDY3 are unknown\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\n        \"term_id\": \"GO:0140096\",\n        \"supporting_discovery_ids\": [0]\n      },\n      {\n        \"term_id\": \"GO:0016787\",\n        \"supporting_discovery_ids\": [0]\n      }\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\n        \"term_id\": \"R-HSA-392499\",\n        \"supporting_discovery_ids\": [0]\n      }\n    ],\n    \"complexes\": [],\n    \"partners\": [],\n    \"other_free_text\": []\n  }\n}\n```"}