{ "uniprot_canonical_ac": "O60294-1", "uniprot_ac": "O60294", "uniprot_id": "TYW4_HUMAN", "mass": { "chemical_mass": 75602.0, "monoisotopic_mass": 75602.0 }, "refseq": { "ac": "NP_055608", "name": "tRNA wybutosine-synthesizing protein 4", "summary": "The protein encoded by this intronless gene belongs to the highly variable methyltransferase superfamily. This gene is the inferred homolog of the Saccharomyces cerevisiae carboxymethyltransferase gene PPM2 that is essential for the synthesis of the hypermodified guanosine Wybutosine (yW). [provided by RefSeq, Jul 2008].", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_055608" }, "gene_names": [ { "name": "LCMT2", "resource": "UniProtKB", "type": "recommended", "url": "https://www.uniprot.org/uniprot/O60294", "id": "O60294" }, { "name": "KIAA0547", "resource": "UniProtKB", "type": "synonym", "url": "https://www.uniprot.org/uniprot/O60294", "id": "O60294" }, { "name": "LCMT2", "resource": "RefSeq", "type": "synonym", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_055608", "id": "NP_055608" }, { "name": "PPM2; TYW4", "resource": "RefSeq", "type": "synonym", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_055608", "id": "NP_055608" }, { "name": "TYW4", "resource": "UniProtKB", "type": "synonym", "url": "https://www.uniprot.org/uniprot/O60294", "id": "O60294" } ], "protein_names": [ { "name": "tRNA wybutosine-synthesizing protein 4", "resource": "UniProtKB", "type": "recommended", "url": "", "id": "O60294" }, { "name": "2.1.1.290", "resource": "UniProtKB", "type": "synonym", "url": "", "id": "O60294" }, { "name": "2.3.1.231", "resource": "UniProtKB", "type": "synonym", "url": "", "id": "O60294" }, { "name": "Leucine carboxyl methyltransferase 2", "resource": "UniProtKB", "type": "synonym", "url": "", "id": "O60294" }, { "name": "tRNA wybutosine-synthesizing protein 4", "resource": "RefSeq", "type": "synonym", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_055608", "id": "NP_055608" }, { "name": "tRNA yW-synthesizing protein 4", "resource": "UniProtKB", "type": "synonym", "url": "", "id": "O60294" }, { "name": "tRNA(Phe) (7-(3-amino-3-(methoxycarbonyl)propyl)wyosine(37)-N)-methoxycarbonyltransferase", "resource": "UniProtKB", "type": "synonym", "url": "", "id": "O60294" }, { "name": "tRNA(Phe) (7-(3-amino-3-carboxypropyl)wyosine(37)-O)-methyltransferase", "resource": "UniProtKB", "type": "synonym", "url": "", "id": "O60294" }, { "name": "tRNA-Wybutosine-synthesizing protein 4; p21WAF1/CIP1 promoter-interacting protein; tRNA(Phe) (7-(3-amino-3-carboxypropyl)wyosine(37)-O)- methyltransferase; tRNA(Phe) (7-(3-amino-3-(methoxycarbonyl)propyl)wyosine(37)-N)- methoxycarbonyltransferase; tRNA-yW synthesizing protein 4", "resource": "RefSeq", "type": "synonym", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_055608", "id": "NP_055608" } ], "function": [ { "annotation": "Kr-pok interacted directly with the DNA binding and oligomerization domains of p53. This interaction was essential for Kr-pok to bind the distal promoter region of the CDKN1A gene, p21WAF1, and to inhibit p53-mediated transcriptional activation of CDKN1A.", "evidence": [ { "database": "RefSeq", "id": "NP_055608", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_055608" }, { "database": "PubMed", "id": "22253232", "url": "https://glygen.org/publication/PubMed/22253232" } ] }, { "annotation": "Probable S-adenosyl-L-methionine-dependent methyltransferase that acts as a component of the wybutosine biosynthesis pathway. Wybutosine is a hyper modified guanosine with a tricyclic base found at the 3'-position adjacent to the anticodon of eukaryotic phenylalanine tRNA (By similarity). May methylate the carboxyl group of leucine residues to form alpha-leucine ester residues.", "evidence": [ { "database": "UniProtKB", "id": "O60294", "url": "https://www.uniprot.org/uniprot/O60294#function" } ] }, { "annotation": "The protein encoded by this intronless gene belongs to the highly variable methyltransferase superfamily. This gene is the inferred homolog of the Saccharomyces cerevisiae carboxymethyltransferase gene PPM2 that is essential for the synthesis of the hypermodified guanosine Wybutosine (yW). [provided by RefSeq, Jul 2008].", "evidence": [ { "database": "RefSeq", "id": "NP_055608", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_055608" } ] }, { "annotation": "This paper reports crystal structures of a yeast homolog, TYW4.", "evidence": [ { "database": "RefSeq", "id": "NP_055608", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_055608" }, { "database": "PubMed", "id": "19287006", "url": "https://glygen.org/publication/PubMed/19287006" } ] } ], "disease": [], "snv": [ { "evidence": [ { "id": "rs1596475207", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1596475207" }, { "id": "rs1596475207", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1596475207" } ], "glycoeffect": [ "n-glyco-sequon-loss", "n-glyco-sequon-gain" ], "start_pos": 17, "end_pos": 17, "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 out of 1 filters: n-glyco-sequon-gain (NTN->NTS).", "chr_id": "15", "chr_pos": "43330440", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N17", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1229735774", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1229735774" }, { "id": "rs1229735774", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1229735774" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "start_pos": 18, "end_pos": 18, "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 out of 1 filters: n-glyco-sequon-gain (DSS->NSS).", "chr_id": "15", "chr_pos": "43330438", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D18", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1347357657", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1347357657" }, { "id": "rs1347357657", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1347357657" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 465, "end_pos": 465, "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 out of 1 filters: o-glyco-site-loss (T->I).", "chr_id": "15", "chr_pos": "43329096", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T465", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "O60294", "database": "BioMuta", "url": "https://hive.biochemistry.gwu.edu/biomuta/proteinview/O60294" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "start_pos": 597, "end_pos": 597, "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "T", "comment": "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (NGK->NGT).", "chr_id": "15", "chr_pos": "43328700", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "K597", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. 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"https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant 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"https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "large intestine cancer", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "O60294", "database": "BioMuta", "url": "https://hive.biochemistry.gwu.edu/biomuta/proteinview/O60294" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "start_pos": 607, "end_pos": 607, "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "H", "sequence_mut": "N", "comment": "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (HSS->NSS).", "chr_id": "15", "chr_pos": "43328671", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "H607", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease 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"http://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs780692032", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780692032" }, { "id": "rs780692032", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780692032" }, { "id": "rs780692032", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780692032#frequency_tab" }, { "id": "rs780692032", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780692032" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "start_pos": 630, "end_pos": 630, "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 out of 1 filters: n-glyco-sequon-gain (DTT->NTT).", "chr_id": "15", "chr_pos": "43328602", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D630", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs554972073", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs554972073" }, { "id": "rs554972073", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs554972073" }, { "id": "rs554972073", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs554972073" }, { "id": "rs554972073", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs554972073" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "start_pos": 678, "end_pos": 678, "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 out of 1 filters: n-glyco-sequon-gain (DLS->NLS).", "chr_id": "15", "chr_pos": "43328458", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.0002", "site_lbl": "D678", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "O60294", "database": "BioMuta", "url": "https://hive.biochemistry.gwu.edu/biomuta/proteinview/O60294" } ], "glycoeffect": [], "start_pos": 82, "end_pos": 82, "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "chr_id": "15", "chr_pos": "43330246", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R82", "disease": [ { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": 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"url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, on chromosome 7", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "predisposing for prostate cancer", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, susceptibility to", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, susceptibility to", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0023122", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0023122", "name": "familial prostate carcinoma", "description": "Prostate carcinoma that has developed in relatives of patients with a history of prostate carcinoma." }, { "id": "MONDO:0023122", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0023122", "name": "familial prostate cancer", "description": "" }, { "id": "MONDO:0023122", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0023122", "name": "hereditary prostate cancer", "description": "" }, { "id": "MONDO:0023122", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0023122", "name": "hereditary prostate carcinoma", "description": "" }, { "id": "MONDO:0023122", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0023122", "name": "prostate cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0023122", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0023122", "name": "prostate cancer, familial, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0023122", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0023122", "name": "prostate cancer, somatic", "description": "" }, { "id": "MONDO:0023122", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0023122", "name": "prostate cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0023122", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0023122", "name": "prostate cancer, familial", "description": "" }, { "id": "MONDO:0023122", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0023122", "name": "prostate cancer, hereditary", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer aggressiveness", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "Prca1", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer susceptibility, X-linked", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" } ] } ] }, { "significant": "No", "trend": "down", "name": "Stomach cancer [DO disease name]", "url": "http://disease-ontology.org/term/DOID:10534", "evidence": [ { "database": "BioXpress", "id": "O60294", "url": "https://hive.biochemistry.gwu.edu/bioxpress/transcriptview/O60294" } ], "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, intestinal", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ] } ] }, { "significant": "No", "trend": "down", "name": "Urinary bladder cancer [DO disease name]", "url": "http://disease-ontology.org/term/DOID:11054", "evidence": [ { "database": "BioXpress", "id": "O60294", "url": "https://hive.biochemistry.gwu.edu/bioxpress/transcriptview/O60294" } ], "disease": [ { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": 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"malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "large intestine cancer", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ] } ] } ], "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60294", "url": "https://www.uniprot.org/uniprot/O60294" } ], "common_name": "Human" } ], "gene": [ { "name": "LCMT2", "url": "https://www.uniprot.org/uniprot/O60294", "locus": { "chromosome": "15", "start_pos": 43323649, "end_pos": 43330582, "strand": "+", "evidence": [ { "database": "Ensembl Gene", "id": "ENSG00000168806", "url": "https://www.ensembl.org/id/ENSG00000168806" } ] } } ], "crossref": [ { "id": "ENSG00000168806", "url": "https://bgee.org/?page=gene&gene_id=ENSG00000168806", "database": "Bgee", "categories": [ "Gene Expression" ] }, { "id": "O60294", "url": "https://hive.biochemistry.gwu.edu/biomuta/proteinview/O60294", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "LCMT2", "url": "http://www.genecards.org/cgi-bin/carddisp.pl?gene=LCMT2", "database": "GeneCards", "categories": [ "Gene Annotation", "Organism-specific" ] }, { "id": "9836", "url": "https://www.ncbi.nlm.nih.gov/gene/9836", "database": "GeneID", "categories": [ "Genome Annotation" ] }, { "id": "17558", "url": "https://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=17558", "database": "HGNC", "categories": [ "Organism-specific" ] }, { "id": "O60294", "url": "https://www.ebi.ac.uk/intact/interactors/id:O60294*", "database": "IntAct", "categories": [ "Other" ] }, { "id": "IPR007213", "url": "https://www.ebi.ac.uk/interpro/entry/IPR007213", "database": "InterPro", "categories": [ "Protein Classification" ] }, { "id": "IPR015915", "url": "https://www.ebi.ac.uk/interpro/entry/IPR015915", "database": "InterPro", "categories": [ "Protein Classification" ] }, { "id": "IPR029063", "url": "https://www.ebi.ac.uk/interpro/entry/IPR029063", "database": "InterPro", "categories": [ "Protein Classification" ] }, { "id": "hsa:9836", "url": "https://www.genome.jp/dbget-bin/get_linkdb?-t+pathway+hsa:9836", "database": "KEGG Pathway", "categories": [ "Enzyme and Pathway" ] }, { "id": "611246", "url": "http://www.omim.org/entry/611246", "database": "MIM", "categories": [ "Other" ] }, { "id": "NX_O60294", "url": "https://www.nextprot.org/entry/NX_O60294", "database": "neXtProt", "categories": [ "Protein", "Organism-specific" ] }, { "id": "O60294", "url": "https://oglcnac.org/atlas/detail/O60294", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "O60294", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O60294", "database": "O-GlcNAc Database", "categories": [ "Glycoproteomics" ] }, { "id": "WEVDFPD", "url": "https://omabrowser.org/oma/group/WEVDFPD/", "database": "OMA", "categories": [ "Protein Classification" ] }, { "id": "5472060at2759", "url": "http://www.orthodb.org/?query=5472060at2759", "database": "OrthoDB", "categories": [ "Protein Classification" ] }, { "id": "PTHR46529", "url": "http://www.pantherdb.org/panther/family.do?clsAccession=PTHR46529", "database": "PANTHER", "categories": [ "Protein Classification" ] }, { "id": "PTHR46529:SF1", "url": "http://www.pantherdb.org/panther/family.do?clsAccession=PTHR46529:SF1", "database": "PANTHER", "categories": [ "Protein Classification" ] }, { "id": "PF04072", "url": "http://pfam.xfam.org/family/PF04072", "database": "Pfam", "categories": [ "Protein Classification" ] }, { "id": "O60294", "url": "https://pharos.nih.gov/targets/O60294", "database": "PHAROS", "categories": [ "Organism-specific" ] }, { "id": "PR_O60294", "url": "http://purl.obolibrary.org/obo/PR_O60294", "database": "PRO", "categories": [ "Protein" ] }, { "id": "R-HSA-6782861", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-6782861", "database": "Reactome", "categories": [ "Protein Classification" ] }, { "id": "NP_055608", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_055608", "database": "RefSeq", "categories": [ "Protein" ] }, { "id": "36903", "url": "https://www.rhea-db.org/rhea/36903", "database": "Rhea", "categories": [ "Enzyme and Pathway" ] }, { "id": "37119", "url": "https://www.rhea-db.org/rhea/37119", "database": "Rhea", "categories": [ "Enzyme and Pathway" ] }, { "id": "H3BU01", "url": "https://www.uniprot.org/uniprot/H3BU01", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "H3BU01-1", "url": "https://www.uniprot.org/uniprot/H3BU01-1", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "O60294", "url": "https://www.uniprot.org/uniprot/O60294", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "O60294-1", "url": "https://www.uniprot.org/uniprot/O60294-1", "database": "UniProtKB", "categories": [ "Protein" ] } ], "sequence": { "sequence": "MGPRSRERRAGAVQNTNDSSALSKRSLAARGYVQDPFAALLVPGAARRAPLIHRGYYVRARAVRHCVRAFLEQIGAPQAALRAQILSLGAGFDSLYFRLKTAGRLARAAVWEVDFPDVARRKAERIGETPELCALTGPFERGEPASALCFESADYCILGLDLRQLQRVEEALGAAGLDAASPTLLLAEAVLTYLEPESAAALIAWAAQRFPNALFVVYEQMRPQDAFGQFMLQHFRQLNSPLHGLERFPDVEAQRRRFLQAGWTACGAVDMNEFYHCFLPAEERRRVENIEPFDEFEEWHLKCAHYFILAASRGDTLSHTLVFPSSEAFPRVNPASPSGVFPASVVSSEGQVPNLKRYGHASVFLSPDVILSAGGFGEQEGRHCRVSQFHLLSRDCDSEWKGSQIGSCGTGVQWDGRLYHTMTRLSESRVLVLGGRLSPVSPALGVLQLHFFKSEDNNTEDLKVTITKAGRKDDSTLCCWRHSTTEVSCQNQEYLFVYGGRSVVEPVLSDWHFLHVGTMAWVRIPVEGEVPEARHSHSACTWQGGALIAGGLGASEEPLNSVLFLRPISCGFLWESVDIQPPITPRYSHTAHVLNGKLLLVGGIWIHSSSFPGVTVINLTTGLSSEYQIDTTYVPWPLMLHNHTSILLPEEQQLLLLGGGGNCFSFGTYFNPHTVTLDLSSLSAGQ", "length": 686, "header": "sp|O60294-1|TYW4_HUMAN Isoform 1 of tRNA wybutosine-synthesizing protein 4 OS=Homo sapiens OX=9606 GN=LCMT2 PE=1 SV=3 CANONICAL=O60294-1" }, "isoforms": [ { "isoform_ac": "H3BU01-1", "url": "", "sequence": { "sequence": "MGPRSRERRAGAVQNTNDSSALSKRSLAARGRTPAGGKY", "length": 39, "header": "tr|H3BU01-1|TYW4_HUMAN Computationally mapped isoform of tRNA wybutosine-synthesizing protein 4 OS=Homo sapiens OX=9606 GN=LCMT2 PE=1 SV=1 CANONICAL=O60294-1" }, "locus": { "chromosome": "15", "start_pos": 43330489, "end_pos": 43329621, "strand": "+", "evidence": [ { "database": "Ensembl Transcript", "id": "ENST00000567039.1", "url": "https://www.ensembl.org/id/ENST00000567039.1" }, { "database": "Ensembl Peptide", "id": "ENSP00000457403.1", "url": "https://www.ensembl.org/id/ENSP00000457403.1" } ] } }, { "isoform_ac": "O60294-1", "url": "", "sequence": { "sequence": "MGPRSRERRAGAVQNTNDSSALSKRSLAARGYVQDPFAALLVPGAARRAPLIHRGYYVRARAVRHCVRAFLEQIGAPQAALRAQILSLGAGFDSLYFRLKTAGRLARAAVWEVDFPDVARRKAERIGETPELCALTGPFERGEPASALCFESADYCILGLDLRQLQRVEEALGAAGLDAASPTLLLAEAVLTYLEPESAAALIAWAAQRFPNALFVVYEQMRPQDAFGQFMLQHFRQLNSPLHGLERFPDVEAQRRRFLQAGWTACGAVDMNEFYHCFLPAEERRRVENIEPFDEFEEWHLKCAHYFILAASRGDTLSHTLVFPSSEAFPRVNPASPSGVFPASVVSSEGQVPNLKRYGHASVFLSPDVILSAGGFGEQEGRHCRVSQFHLLSRDCDSEWKGSQIGSCGTGVQWDGRLYHTMTRLSESRVLVLGGRLSPVSPALGVLQLHFFKSEDNNTEDLKVTITKAGRKDDSTLCCWRHSTTEVSCQNQEYLFVYGGRSVVEPVLSDWHFLHVGTMAWVRIPVEGEVPEARHSHSACTWQGGALIAGGLGASEEPLNSVLFLRPISCGFLWESVDIQPPITPRYSHTAHVLNGKLLLVGGIWIHSSSFPGVTVINLTTGLSSEYQIDTTYVPWPLMLHNHTSILLPEEQQLLLLGGGGNCFSFGTYFNPHTVTLDLSSLSAGQ", "length": 686, "header": "sp|O60294-1|TYW4_HUMAN Isoform 1 of tRNA wybutosine-synthesizing protein 4 OS=Homo sapiens OX=9606 GN=LCMT2 PE=1 SV=3 CANONICAL=O60294-1" }, "locus": { "chromosome": "15", "start_pos": 43330489, "end_pos": 43328432, "strand": "+", "evidence": [ { "database": "Ensembl Transcript", "id": "ENST00000305641.7", "url": "https://www.ensembl.org/id/ENST00000305641.7" }, { "database": "Ensembl Peptide", "id": "ENSP00000307214.5", "url": "https://www.ensembl.org/id/ENSP00000307214.5" } ] } } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "site_category": "reported_with_glycan", "site_seq": "T", "relation": "attached", "comment": "O-GlcNAcylation", "start_pos": 465, "start_aa": "Thr", "end_pos": 465, "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr465", "evidence": [ { "id": "O60294", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O60294" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "O60294", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/O60294" } ] } ], "phosphorylation": [], "glycation": [], "keywords": [ "enzyme", "glycoprotein", "glycoprotein_reported_with_glycan" ], "publication": [ { "title": "p53RFP, a p53-inducible RING-finger protein, regulates the stability of p21WAF1.", "journal": "Oncogene", "date": "2003", "authors": "Ng CC, Arakawa H, Fukuda S, Kondoh H, Nakamura Y", "evidence": [ { "database": "UniProtKB", "id": "O60294", "url": "https://www.uniprot.org/uniprot/O60294" } ], "reference": [ { "type": "PubMed", "id": "12853982", "url": "https://glygen.org/publication/PubMed/12853982" } ] }, { "title": "Isolation and characterization of the human tRNA-(N1G37) methyltransferase (TRM5) and comparison to the Escherichia coli TrmD protein.", "journal": "Biochemistry", "date": "2004", "authors": "Brule H, Elliott M, Redlak M, Zehner ZE, Holmes WM", "evidence": [ { "database": "Reactome", "id": "R-HSA-6782861", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-6782861" } ], "reference": [ { "type": "PubMed", "id": "15248782", "url": "https://glygen.org/publication/PubMed/15248782" } ] }, { "title": "Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4.", "journal": "Nucleic acids research", "date": "2009", "authors": "Suzuki Y, Noma A, Suzuki T, Ishitani R, Nureki O", "evidence": [ { "database": "RefSeq", "id": "NP_055608", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_055608" } ], "reference": [ { "type": "PubMed", "id": "19287006", "url": "https://glygen.org/publication/PubMed/19287006" } ] }, { "title": "Expanding role of the jumonji C domain as an RNA hydroxylase.", "journal": "The Journal of biological chemistry", "date": "2010", "authors": "Noma A, Ishitani R, Kato M, Nagao A, Nureki O, Suzuki T", "evidence": [ { "database": "Reactome", "id": "R-HSA-6782861", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-6782861" } ], "reference": [ { "type": "PubMed", "id": "20739293", "url": "https://glygen.org/publication/PubMed/20739293" } ] }, { "title": "Crystal structure of a novel JmjC-domain-containing protein, TYW5, involved in tRNA modification.", "journal": "Nucleic acids research", "date": "2011", "authors": "Kato M, Araiso Y, Noma A, Nagao A, Suzuki T, Ishitani R, Nureki O", "evidence": [ { "database": "Reactome", "id": "R-HSA-6782861", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-6782861" } ], "reference": [ { "type": "PubMed", "id": "20972222", "url": "https://glygen.org/publication/PubMed/20972222" } ] }, { "title": "KR-POK interacts with p53 and represses its ability to activate transcription of p21WAF1/CDKN1A.", "journal": "Cancer research", "date": "2012", "authors": "Jeon BN, Kim MK, Choi WI, Koh DI, Hong SY, Kim KS, Kim M, Yun CO, Yoon J, Choi KY, Lee KR, Nephew KP, Hur MW", "evidence": [ { "database": "RefSeq", "id": "NP_055608", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_055608" } ], "reference": [ { "type": "PubMed", "id": "22253232", "url": "https://glygen.org/publication/PubMed/22253232" } ] }, { "title": "Structure-function analysis of human TYW2 enzyme required for the biosynthesis of a highly modified Wybutosine (yW) base in phenylalanine-tRNA.", "journal": "PloS one", "date": "2012", "authors": "Rodriguez V, Vasudevan S, Noma A, Carlson BA, Green JE, Suzuki T, Chandrasekharappa SC", "evidence": [ { "database": "Reactome", "id": "R-HSA-6782861", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-6782861" } ], "reference": [ { "type": "PubMed", "id": "22761755", "url": "https://glygen.org/publication/PubMed/22761755" } ] }, { "title": "Conservation of structure and mechanism by Trm5 enzymes.", "journal": "RNA (New York, N.Y.)", "date": "2013", "authors": "Christian T, Gamper H, Hou YM", "evidence": [ { "database": "Reactome", "id": "R-HSA-6782861", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-6782861" } ], "reference": [ { "type": "PubMed", "id": "23887145", "url": "https://glygen.org/publication/PubMed/23887145" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "O60294", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O60294" }, { "database": "O-GlcNAc Atlas", "id": "O60294", "url": "https://oglcnac.org/atlas/detail/O60294" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] } ], "pathway": [ { "id": "hsa:9836", "name": "", "url": "https://www.genome.jp/dbget-bin/get_linkdb?-t+pathway+hsa:9836", "resource": "KEGG Pathway" }, { "id": "R-HSA-6782861", "name": "Synthesis of wybutosine at G37 of tRNA(Phe)", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-6782861", "resource": "Reactome", "description": "Synthesis of wybutosine at G37 of tRNA(Phe)" } ], "orthologs": [ { "uniprot_canonical_ac": "Q5XIA3-1", "protein_name": "tRNA wybutosine-synthesizing protein 4", "gene_name": "Lcmt2", "tax_id": 10116, "organism": "Rattus norvegicus", "sequence": { "sequence": "MGPRSRQRRTGTVQSTNDSSSLSKRSLAAQGYVSDAFAPLLVPGIVRRTPLIHRGYYVRARAVRHCVRAFLDLTGAIRSPTRAQILSLGSGSDSLYFRLKAAGLLTRTAVWEVDFPDVSRLKAKRIEETPELCAQTGPFKIGDSASTLCFESSDYRILGADLRELQRLGEALDSAGLDATSPTLILAEAVLTYLEPSRAAALIAWVAQRFPNALFVIYEQMKPGDAFGQIMLQHFRRLNSPLHGLELFPDVEAQRQRFLQAGWTTCSALDLNEFYRRLIPADERRRVETLEPFDEFEEWHLKCSHYFILAASRGDILSETPVFLPSEASFQIDPALPSGFLSASVVTSDHQHSSLQRYGHTSVLLSPGIIFSAGGFGEQEGRHCRVSRFHLLSRSCDSEWKGCQISTLGTEGQWDGRLYHTMTRLSDTRVLVLGGRLSPVNPASGALQLDIYKSEDNCPEGQNVVVTKAALEEGSMLSCWRHSTTEVYYQNQRYLFVYGGRSVTDPVLSDCRFLHVETMAWVRIPVQGSSPEGRHSHSACSWQGGALIAGGLGASEEPLSSVFFLRPVSSGFLWESIHIQPSITPRYSHTAHVFNGKLLLVGGVWIHSSSVPGVTVISLTTGLSSEYQIDTASVPWPLMLHNHSSALLPEEQQLLLIGGGGNCFSFGTYFNPHTVGLDLSSLGLGQ", "length": 686 }, "evidence": [ { "id": "45923818", "url": "http://www.informatics.jax.org/homology/45923818", "database": "MGI" }, { "id": "O60294", "url": "https://omabrowser.org/oma/group/O60294/", "database": "OMA" } ], "common_name": "Rat" }, { "uniprot_canonical_ac": "Q8BYR1-1", "protein_name": "tRNA wybutosine-synthesizing protein 4", "gene_name": "Lcmt2", "tax_id": 10090, "organism": "Mus musculus", "sequence": { "sequence": "MGPRGRQRRAGTVQSTNDSSSLSKRSLAAHGYVRDPFAALLVPGPVRRTPLIHRGYYVRARAVRHCVRAFLELTSALPSRTRAQILSLGSGSDSLYFRLKAAGLLARAAVWEVDFPDVSRLKAERIEETPELRAQTGPFKIGDSASSLCFESADYRILGADLRELQRLGEALDGAGLDATSPTLLLAEAVLTYLEPSSATALIAWAAQRFPDALFVIYEQMQPGDAFGQIMLQHFQRLHSPLHGLELFPVVKAQRQRFLQAGWTACSALDLNEFYRRLLSAEERQRVETLEPFDEYEEWHLKCSHYFILAASRGDILSETPVFEPSEASFQIDPASPSGFLSARVVTSDHQHSSLKRYGHASALLSPGVIFSAGGFGEQEGRHCRVSRFHVLSRSCDSEWEGCQISTLGTEGQWDGRLYHTMTRLSDTRVLVLGGRLSPVSPASGALQLDLYKSKDNCSEGQNVTVTKAALEEGSVLSCWRHSTTEVYYQNQRYLFVYGGRSVAEPVLSDCRFLHVETMAWVRIPVQGASPEGRHSHSACSWQGGALIAGGLGASEELLSSVLFLKPVSSGFLWESIDIQPSITPRYSHTAHVFNGKLLLVGGVWIHSSSVPGVTVICLTTGLSSEYQIDTASVPWPLMLHNHSSALLPEEQQLLLIGGGGNCFSFGTYFNPHTVALDLSSLRSGQ", "length": 686 }, "evidence": [ { "id": "45923818", "url": "http://www.informatics.jax.org/homology/45923818", "database": "MGI" }, { "id": "O60294", "url": "https://omabrowser.org/oma/group/O60294/", "database": "OMA" } ], "common_name": "Mouse" } ], "go_annotation": { "categories": [ { "name": "Molecular Function", "total": 2, "go_terms": [ { "name": "tRNA methyltransferase activity", "id": "GO:0008175", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0008175", "evidence": [ { "database": "UniProtKB", "id": "O60294", "url": "https://www.uniprot.org/uniprot/O60294" } ], "pmid": "" }, { "name": "S-adenosylmethionine-dependent methyltransferase activity", "id": "GO:0008757", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0008757", "evidence": [ { "database": "UniProtKB", "id": "O60294", "url": "https://www.uniprot.org/uniprot/O60294" } ], "pmid": "" } ] }, { "name": "Cellular Component", "total": 1, "go_terms": [ { "name": "cytoplasm", "id": "GO:0005737", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0005737", "evidence": [ { "database": "UniProtKB", "id": "O60294", "url": "https://www.uniprot.org/uniprot/O60294" } ], "pmid": "" } ] }, { "name": "Biological Process", "total": 3, "go_terms": [ { "name": "tRNA modification", "id": "GO:0006400", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0006400", "evidence": [ { "database": "UniProtKB", "id": "O60294", "url": "https://www.uniprot.org/uniprot/O60294" } ], "pmid": "" }, { "name": "tRNA methylation", "id": "GO:0030488", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0030488", "evidence": [ { "database": "UniProtKB", "id": "O60294", "url": "https://www.uniprot.org/uniprot/O60294" } ], "pmid": "" }, { "name": "wybutosine biosynthetic process", "id": "GO:0031591", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0031591", "evidence": [ { "database": "UniProtKB", "id": "O60294", "url": "https://www.uniprot.org/uniprot/O60294" } ], "pmid": "" } ] } ] }, "pro_annotation": [], "site_annotation": [ { "start_pos": 17, "end_pos": 19, "annotation": "n_glycosylation_sequon" }, { "start_pos": 457, "end_pos": 459, "annotation": "n_glycosylation_sequon" }, { "start_pos": 618, "end_pos": 620, "annotation": "n_glycosylation_sequon" }, { "start_pos": 642, "end_pos": 644, "annotation": "n_glycosylation_sequon" } ], "ptm_annotation": [], "interactions": [], "reactions": [ { "id": "36903", "name": "", "equation": "7-[(3S)-3-amino-3-carboxypropyl]wyosine(37) in tRNA(Phe) + S-adenosyl-L-methionine = 7-[(3S)-(3-amino-3-methoxycarbonyl)propyl]wyosine(37) in tRNA(Phe) + S-adenosyl-L-homocysteine", "summary": "", "cellular_location": "", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "Q5XIA3-1", "O60294-1", "Q8BYR1-1", "Q08282-1" ], "evidence": [ { "id": "36903", "database": "Rhea", "url": "https://www.rhea-db.org/rhea/36903" } ] }, { "id": "37119", "name": "", "equation": "7-[(3S)-(3-amino-3-methoxycarbonyl)propyl]wyosine(37) in tRNA(Phe) + CO2 + S-adenosyl-L-methionine = 2 H(+) + S-adenosyl-L-homocysteine + wybutosine(37) in tRNA(Phe)", "summary": "", "cellular_location": "", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "Q5XIA3-1", "O60294-1", "Q8BYR1-1", "Q08282-1" ], "evidence": [ { "id": "37119", "database": "Rhea", "url": "https://www.rhea-db.org/rhea/37119" } ] }, { "id": "R-HSA-6782881", "name": "LCMT2 methylates yW-72 yielding yW-58 at nucleotide 37 of tRNA(Phe)", "equation": "", "summary": "As inferred from homologues in Saccharomyces cerevisiae, LCMT2 (TYW4) transfers a methyl group from S-adenosylmethionine to yW-72 (7-((3S)-3-amino-3-carboxypropyl)wyosine) at nucleotide 37 of tRNA(Phe), yielding yW-58 (7-((3S)-3-amino-3-(methoxycarbonyl)propyl)wyosine) and S-adenosylhomocysteine.", "cellular_location": "cytoplasm", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "O60294-1" ], "evidence": [ { "id": "R-HSA-6782881", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-6782881" } ] }, { "id": "R-HSA-6782890", "name": "LCMT2 methoxycarbonylates yW-58 yielding yW (wybutosine) at nucleotide 37 of tRNA(Phe)", "equation": "", "summary": "As inferred from homologues in Saccharomyces cerevisiae, LCMT2 (TYW4) methoxycarbonylates yW-58 (7-((3S)-3-amino-3-(methoxycarbonyl)propyl)wyosine) at nucleotide 37 of tRNA(Phe) yielding yW (wybutosine). A molecule of carbon dioxide is incorporated during the reaction.", "cellular_location": "cytoplasm", "input_participant_list": [ "R-HSA-6782864" ], "output_participant_list": [ "R-ALL-5278409", "R-HSA-6782903" ], "enzyme_list": [ "O60294-1" ], "evidence": [ { "id": "R-HSA-6782890", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-6782890" } ] }, { "id": "R-HSA-6783473", "name": "LCMT2 methoxycarbonylates OHyW-72 yielding OHyW (hydroxywybutosine) at nucleotide 37 of tRNA(Phe)", "equation": "", "summary": "LCMT2 (TYW4) methoxycarbonylates OHyW-72 (7-(2-hydroxy-3-amino-3-carboxypropyl)wyosine) at nucleotide 37 of tRNA(Phe), yielding OHyW (hydroxywybutosine) (Noma et al. 2010).", "cellular_location": "cytoplasm", "input_participant_list": [], "output_participant_list": [ "R-HSA-6783457" ], "enzyme_list": [ "O60294-1" ], "evidence": [ { "id": "R-HSA-6783473", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-6783473" } ] } ], "reaction_participants": [ { "participant_id": "R-ALL-5278409", "participant_name": "AdoHcy [cytoplasm]", "crossref": [ { "id": "C00021", "database": "COMPOUND", "url": "" }, { "id": "5265", "database": "Guide to Pharmacology - Ligands", "url": "" }, { "id": "11533261", "database": "PubChem Substance", "url": "" }, { "id": "16680", "database": "ChEBI", "url": "" }, { "id": "HMDB0000939", "database": "HMDB Metabolite", "url": "" }, { "id": "000004228232", "database": "ZINC", "url": "" }, { "id": "16680", "database": "ChEBI", "url": "" }, { "id": "11533261", "database": "PubChem Substance", "url": "" }, { "id": "000004228232", "database": "ZINC", "url": "" }, { "id": "C00021", "database": "COMPOUND", "url": "" }, { "id": "HMDB0000939", "database": "HMDB Metabolite", "url": "" }, { "id": "5265", "database": "Guide to Pharmacology - Ligands", "url": "" } ] }, { "participant_id": "R-HSA-6782864", "participant_name": "tRNA(Phe) containing yW-58 at 37 [cytoplasm]", "crossref": [ { "id": "29184", "database": "ChEBI", "url": "" }, { "id": "74275", "database": "ChEBI", "url": "" } ] }, { "participant_id": "R-HSA-6782903", "participant_name": "tRNA(Phe) containing yW at 37 [cytoplasm]", "crossref": [ { "id": "73544", "database": "ChEBI", "url": "" }, { "id": "29184", "database": "ChEBI", "url": "" } ] }, { "participant_id": "R-HSA-6783457", "participant_name": "tRNA(Phe) containing OHyW at 37 [cytoplasm]", "crossref": [ { "id": "29184", "database": "ChEBI", "url": "" }, { "id": "73602", "database": "ChEBI", "url": "" } ] } ], "reaction_enzymes": [ { "uniprot_ac": "O60294", "gene_name": "LCMT2", "activity": [ { "ec_number": "2.1.1.290", "activity": "7-[(3S)-3-amino-3-carboxypropyl]wyosine(37) in tRNA(Phe) + S-adenosyl-L-methionine = 7-[(3S)-(3-amino-3-methoxycarbonyl)propyl]wyosine(37) in tRNA(Phe) + S-adenosyl-L-homocysteine.", "evidence": [ { "id": "O60294", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/O60294" } ] }, { "ec_number": "2.3.1.231", 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