{ "uniprot_canonical_ac": "O95025-1", "uniprot_ac": "O95025", "uniprot_id": "SEM3D_HUMAN", "mass": { "chemical_mass": 89651.0, "monoisotopic_mass": 89651.0 }, "refseq": { "ac": "NP_689967", "name": "semaphorin-3D precursor", "summary": "This gene encodes a member of the semaphorin III family of secreted signaling proteins that are involved in axon guidance during neuronal development. The encoded protein contains an N-terminal Sema domain, an immunoglobulin like domain and a C-terminal basic domain. The protein encoded by this gene binds neuropilin and plays an important role in cardiovascular development. [provided by RefSeq, Aug 2016].", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_689967" }, "gene_names": [ { "name": "SEMA3D", "resource": "UniProtKB", "type": "recommended", "url": "https://www.uniprot.org/uniprot/O95025", "id": "O95025" }, { "name": "PRO1491", "resource": "UniProtKB", "type": "synonym", "url": "https://www.uniprot.org/uniprot/O95025", "id": "O95025" }, { "name": "SEMA3D", "resource": "RefSeq", "type": "synonym", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_689967", "id": "NP_689967" }, { "name": "coll-2; Sema-Z2", "resource": "RefSeq", "type": "synonym", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_689967", "id": "NP_689967" } ], "protein_names": [ { "name": "Semaphorin-3D", "resource": "UniProtKB", "type": "recommended", "url": "", "id": "O95025" }, { "name": "collapsin 2; sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D", "resource": "RefSeq", "type": "synonym", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_689967", "id": "NP_689967" }, { "name": "semaphorin-3D precursor", "resource": "RefSeq", "type": "synonym", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_689967", "id": "NP_689967" } ], "function": [ { "annotation": "Induces the collapse and paralysis of neuronal growth cones. Could potentially act as repulsive cues toward specific neuronal populations. Binds to neuropilin (By similarity).", "evidence": [ { "database": "UniProtKB", "id": "O95025", "url": "https://www.uniprot.org/uniprot/O95025#function" } ] }, { "annotation": "Low SEMA3D expression is associated with colorectal cancer. Publication Status: Online-Only", "evidence": [ { "database": "RefSeq", "id": "NP_689967", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_689967" }, { "database": "PubMed", "id": "28320475", "url": "https://glygen.org/publication/PubMed/28320475" } ] }, { "annotation": "Novel mutation in SEMA3D segregates with the complete phenotype with variable expressivity in two pedigrees with autosomal dominant familial Meniere's disease.", "evidence": [ { "database": "RefSeq", "id": "NP_689967", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_689967" }, { "database": "PubMed", "id": "27876815", "url": "https://glygen.org/publication/PubMed/27876815" } ] }, { "annotation": "Observational study of gene-disease association. (HuGE Navigator)", "evidence": [ { "database": "RefSeq", "id": "NP_689967", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_689967" }, { "database": "PubMed", "id": "19054571", "url": "https://glygen.org/publication/PubMed/19054571" } ] }, { "annotation": "SEMA3D mRNA is expressed mainly in the cytoplasm of the endometrial cancer cells. Publication Status: Online-Only", "evidence": [ { "database": "RefSeq", "id": "NP_689967", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_689967" }, { "database": "PubMed", "id": "29074988", "url": "https://glygen.org/publication/PubMed/29074988" } ] }, { "annotation": "Sema3D inhibits tumor development from MDA-MB-231 and MDA-MB-435 cancer cells. It inhibits tumor angiogenesis in all of the formed tumors. Publication Status: Online-Only", "evidence": [ { "database": "RefSeq", "id": "NP_689967", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_689967" }, { "database": "PubMed", "id": "18818766", "url": "https://glygen.org/publication/PubMed/18818766" } ] }, { "annotation": "Semaphorin 3D inhibits proliferation and migration of papillary thyroid carcinoma by regulating MAPK/ERK signaling pathway.", "evidence": [ { "database": "RefSeq", "id": "NP_689967", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_689967" }, { "database": "PubMed", "id": "35190928", "url": "https://glygen.org/publication/PubMed/35190928" } ] }, { "annotation": "This gene encodes a member of the semaphorin III family of secreted signaling proteins that are involved in axon guidance during neuronal development. The encoded protein contains an N-terminal Sema domain, an immunoglobulin like domain and a C-terminal basic domain. The protein encoded by this gene binds neuropilin and plays an important role in cardiovascular development. [provided by RefSeq, Aug 2016].", "evidence": [ { "database": "RefSeq", "id": "NP_689967", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_689967" } ] }, { "annotation": "This study provided strong evidence that SEMA3D confers susceptibility to schizophrenia, which could contribute to the neurodevelopmental impairments in the disorder. GeneRIF: Observational study of gene-disease association. (HuGE Navigator)", "evidence": [ { "database": "RefSeq", "id": "NP_689967", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_689967" }, { "database": "PubMed", "id": "20684831", "url": "https://glygen.org/publication/PubMed/20684831" } ] }, { "annotation": "Tumor-derived semaphorin 3D promoting cancer cachexia via regulating hypothalamic pro-opiomelanocortin neurons.", "evidence": [ { "database": "RefSeq", "id": "NP_689967", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_689967" }, { "database": "PubMed", "id": "37219490", "url": "https://glygen.org/publication/PubMed/37219490" } ] } ], "disease": [], "snv": [ { "evidence": [ { "id": "rs768986154", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768986154" }, { "id": "rs768986154", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768986154" }, { "id": "rs768986154", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs768986154#frequency_tab" }, { "id": "rs768986154", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768986154" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "start_pos": 139, "end_pos": 139, "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 out of 1 filters: n-glyco-sequon-loss (NKT->DKT).", "chr_id": "7", "chr_pos": "85073042", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N139", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1029763874", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1029763874" }, { "id": "rs1029763874", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1029763874#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "start_pos": 139, "end_pos": 139, "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 out of 1 filters: n-glyco-sequon-loss (NKT->KKT).", "chr_id": "7", "chr_pos": "85073040", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N139", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1250965338", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1250965338" }, { "id": "rs1250965338", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1250965338" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "start_pos": 141, "end_pos": 141, "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 out of 1 filters: n-glyco-sequon-loss (NKT->NKI).", "chr_id": "7", "chr_pos": "85073035", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T141", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1583887578", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1583887578" }, { "id": "rs1583887578", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1583887578" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "start_pos": 231, "end_pos": 231, "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 out of 1 filters: n-glyco-sequon-gain (DIS->NIS).", "chr_id": "7", "chr_pos": "85065451", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D231", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "O95025", "database": "BioMuta", "url": "https://hive.biochemistry.gwu.edu/biomuta/proteinview/O95025" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "start_pos": 241, "end_pos": 241, "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (NGA->NGT).", "chr_id": "7", "chr_pos": "85055857", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A241", "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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"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 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"https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "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" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ] }, { "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. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "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 large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "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" } ] }, { "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 Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs759628275", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759628275" }, { "id": "rs759628275", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759628275" }, { "id": "rs759628275", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759628275" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "start_pos": 763, "end_pos": 763, "sequence_org": "R", 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"evidence": [ { "database": "Bgee", "id": "ENSG00000153993", "url": "https://bgee.org/?page=gene&gene_id=ENSG00000153993" } ] }, { "tissue": { "name": "Colon", "namespace": "UBERON", "id": "0001155", "url": "http://purl.obolibrary.org/obo/UBERON_0001155" }, "score": "47.76", "present": "LOW", "evidence": [ { "database": "Bgee", "id": "ENSG00000153993", "url": "https://bgee.org/?page=gene&gene_id=ENSG00000153993" } ] }, { "tissue": { "name": "Urinary bladder", "namespace": "UBERON", "id": "0001255", "url": "http://purl.obolibrary.org/obo/UBERON_0001255" }, "score": "65.86", "present": "MEDIUM", "evidence": [ { "database": "Bgee", "id": "ENSG00000153993", "url": "https://bgee.org/?page=gene&gene_id=ENSG00000153993" } ] }, { "tissue": { "name": "Thyroid gland", "namespace": "UBERON", "id": "0002046", "url": "http://purl.obolibrary.org/obo/UBERON_0002046" }, "score": "83.07", "present": "HIGH", "evidence": [ { "database": "Bgee", "id": "ENSG00000153993", "url": 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"sequence": "MNANKDERLKARSQDFHLFPALMMLSMTMLFLPVTGTLKQNIPRLKLTYKDLLLSNSCIPFLGSSEGLDFQTLLLDEERGRLLLGAKDHIFLLSLVDLNKNFKKIYWPAAKERVELCKLAGKDANTECANFIRVLQPYNKTHIYVCGTGAFHPICGYIDLGVYKEDIIFKLDTHNLESGRLKCPFDPQQPFASVMTDEYLYSGTASDFLGKDTAFTRSLGPTHDHHYIRTDISEHYWLNGAKFIGTFFIPDTYNPDDDKIYFFFRESSQEGSTSDKTILSRVGRVCKENLCFED", "length": 294, "header": "tr|C9JYT6-1|SEM3D_HUMAN Computationally mapped isoform of Semaphorin-3D OS=Homo sapiens OX=9606 GN=SEMA3D PE=2 SV=1 CANONICAL=O95025-1" }, "locus": { "chromosome": "7", "start_pos": 85121891, "end_pos": 85050730, "strand": "+", "evidence": [ { "database": "Ensembl Transcript", "id": "ENST00000444867.1", "url": "https://www.ensembl.org/id/ENST00000444867.1" }, { "database": "Ensembl Peptide", "id": "ENSP00000401366.1", "url": "https://www.ensembl.org/id/ENSP00000401366.1" } ] } }, { "isoform_ac": "O95025-1", "url": "", "sequence": { "sequence": "MNANKDERLKARSQDFHLFPALMMLSMTMLFLPVTGTLKQNIPRLKLTYKDLLLSNSCIPFLGSSEGLDFQTLLLDEERGRLLLGAKDHIFLLSLVDLNKNFKKIYWPAAKERVELCKLAGKDANTECANFIRVLQPYNKTHIYVCGTGAFHPICGYIDLGVYKEDIIFKLDTHNLESGRLKCPFDPQQPFASVMTDEYLYSGTASDFLGKDTAFTRSLGPTHDHHYIRTDISEHYWLNGAKFIGTFFIPDTYNPDDDKIYFFFRESSQEGSTSDKTILSRVGRVCKNDVGGQRSLINKWTTFLKARLICSIPGSDGADTYFDELQDIYLLPTRDERNPVVYGVFTTTSSIFKGSAVCVYSMADIRAVFNGPYAHKESADHRWVQYDGRIPYPRPGTCPSKTYDPLIKSTRDFPDDVISFIKRHSVMYKSVYPVAGGPTFKRINVDYRLTQIVVDHVIAEDGQYDVMFLGTDIGTVLKVVSISKEKWNMEEVVLEELQIFKHSSIILNMELSLKQQQLYIGSRDGLVQLSLHRCDTYGKACADCCLARDPYCAWDGNACSRYAPTSKRRARRQDVKYGDPITQCWDIEDSISHETADEKVIFGIEFNSTFLECIPKSQQATIKWYIQRSGDEHREELKPDERIIKTEYGLLIRSLQKKDSGMYYCKAQEHTFIHTIVKLTLNVIENEQMENTQRAEHEEGKVKDLLAESRLRYKDYIQILSSPNFSLDQYCEQMWHREKRRQRNKGGPKWKHMQEMKKKRNRRHHRDLDELPRAVAT", "length": 777, "header": "sp|O95025-1|SEM3D_HUMAN Isoform 1 of Semaphorin-3D OS=Homo sapiens OX=9606 GN=SEMA3D PE=2 SV=2 CANONICAL=O95025-1" }, "locus": { "chromosome": "7", "start_pos": 85121891, "end_pos": 84999443, "strand": "+", "evidence": [ { "database": "Ensembl Transcript", "id": "ENST00000284136.11", "url": "https://www.ensembl.org/id/ENST00000284136.11" }, { "database": "Ensembl Peptide", "id": "ENSP00000284136.6", "url": "https://www.ensembl.org/id/ENSP00000284136.6" } ] } } ], "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "site_category": "predicted", "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "start_pos": 139, "start_aa": "Asn", "end_pos": 139, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn139", "evidence": [ { "id": "O95025", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/O95025#ptm_processing" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "site_category": "predicted", "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "start_pos": 607, "start_aa": "Asn", "end_pos": 607, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn607", "evidence": [ { "id": "O95025", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/O95025#ptm_processing" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "site_category": "predicted", "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "start_pos": 724, "start_aa": "Asn", "end_pos": 724, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn724", "evidence": [ { "id": "O95025", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/O95025#ptm_processing" } ] }, { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "site_category": "reported_with_glycan", "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "evidence": [ { "id": "O95025", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95025" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" } ] } ], "phosphorylation": [ { "start_pos": 447, "end_pos": 447, "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O95025", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95025" }, { "database": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ], "site_lbl": "Tyr447" } ], "glycation": [], "keywords": [ "glycoprotein", "glycoprotein_predicted", "glycoprotein_reported_with_glycan" ], "publication": [ { "title": "The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment.", "journal": "Genome Res.", "date": "2003", "authors": "Clark HF, Gurney AL, Abaya E, Baker K, Baldwin D, Brush J, Chen J, Chow B, Chui C, Crowley C, Currell B, Deuel B, Dowd P, Eaton D, Foster J, Grimaldi C, Gu Q, Hass PE, Heldens S, Huang A, Kim HS, Klimowski L, Jin Y, Johnson S, Lee J, Lewis L, Liao D, Mark M, Robbie E, Sanchez C, Schoenfeld J, Seshagiri S, Simmons L, Singh J, Smith V, Stinson J, Vagts A, Vandlen R, Watanabe C, Wieand D, Woods K, Xie MH, Yansura D, Yi S, Yu G, Yuan J, Zhang M, Zhang Z, Goddard A, Wood WI, Godowski P, Gray A", "evidence": [ { "database": "UniProtKB", "id": "O95025", "url": "https://www.uniprot.org/uniprot/O95025" } ], "reference": [ { "type": "PubMed", "id": "12975309", "url": "https://glygen.org/publication/PubMed/12975309" } ] }, { "title": "Successful inhibition of tumor development by specific class-3 semaphorins is associated with expression of appropriate semaphorin receptors by tumor cells.", "journal": "PloS one", "date": "2008", "authors": "Kigel B, Varshavsky A, Kessler O, Neufeld G", "evidence": [ { "database": "RefSeq", "id": "NP_689967", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_689967" } ], "reference": [ { "type": "PubMed", "id": "18818766", "url": "https://glygen.org/publication/PubMed/18818766" } ] }, { "title": "Polymorphisms in genes involved in neurodevelopment may be associated with altered brain morphology in schizophrenia: preliminary evidence.", "journal": "Psychiatry research", "date": "2009", "authors": "Gregorio SP, Sallet PC, Do KA, Lin E, Gattaz WF, Dias-Neto E", "evidence": [ { "database": "RefSeq", "id": "NP_689967", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_689967" } ], "reference": [ { "type": "PubMed", "id": "19054571", "url": "https://glygen.org/publication/PubMed/19054571" } ] }, { "title": "Phosphoproteomic analysis of human embryonic stem cells.", "journal": "Cell stem cell", "date": "2009", "authors": "Brill LM, Xiong W, Lee KB, Ficarro SB, Crain A, Xu Y, Terskikh A, Snyder EY, Ding S", "evidence": [ { "database": "iPTMnet", "id": "O95025", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95025" } ], "reference": [ { "type": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ] }, { "title": "Possible association of the semaphorin 3D gene (SEMA3D) with schizophrenia.", "journal": "Journal of psychiatric research", "date": "2011", "authors": "Fujii T, Uchiyama H, Yamamoto N, Hori H, Tatsumi M, Ishikawa M, Arima K, Higuchi T, Kunugi H", "evidence": [ { "database": "RefSeq", "id": "NP_689967", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_689967" } ], "reference": [ { "type": "PubMed", "id": "20684831", "url": "https://glygen.org/publication/PubMed/20684831" } ] }, { "title": "Variable expressivity and genetic heterogeneity involving DPT and SEMA3D genes in autosomal dominant familial Meniere's disease.", "journal": "European journal of human genetics : EJHG", "date": "2017", "authors": "Martin-Sierra C, Gallego-Martinez A, Requena T, Frejo L, Batuecas-Caletrio A, Lopez-Escamez JA", "evidence": [ { "database": "RefSeq", "id": "NP_689967", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_689967" } ], "reference": [ { "type": "PubMed", "id": "27876815", "url": "https://glygen.org/publication/PubMed/27876815" } ] }, { "title": "Decreased expression of semaphorin 3D is associated with genesis and development in colorectal cancer.", "journal": "World journal of surgical oncology", "date": "2017", "authors": "Wang Z, Ding M, Qian N, Song B, Yu J, Tang J, Wang J", "evidence": [ { "database": "RefSeq", "id": "NP_689967", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_689967" } ], "reference": [ { "type": "PubMed", "id": "28320475", "url": "https://glygen.org/publication/PubMed/28320475" } ] }, { "title": "Promoter-level transcriptome in primary lesions of endometrial cancer identified biomarkers associated with lymph node metastasis.", "journal": "Scientific reports", "date": "2017", "authors": "Yoshida E, Terao Y, Hayashi N, Mogushi K, Arakawa A, Tanaka Y, Ito Y, Ohmiya H, Hayashizaki Y, Takeda S, Itoh M, Kawaji H", "evidence": [ { "database": "RefSeq", "id": "NP_689967", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_689967" } ], "reference": [ { "type": "PubMed", "id": "29074988", "url": "https://glygen.org/publication/PubMed/29074988" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "O95025", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95025" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "O95025", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95025" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "Semaphorin 3D inhibits proliferation and migration of papillary thyroid carcinoma by regulating MAPK/ERK signaling pathway.", "journal": "Molecular biology reports", "date": "2022", "authors": "Hai R, You Q, Wu F, Qiu G, Yang Q, Shu L, Xie L, Zhou X", "evidence": [ { "database": "RefSeq", "id": "NP_689967", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_689967" } ], "reference": [ { "type": "PubMed", "id": "35190928", "url": "https://glygen.org/publication/PubMed/35190928" } ] }, { "title": "Tumor-derived semaphorin 3D promoting cancer cachexia via regulating hypothalamic pro-opiomelanocortin neurons.", "journal": "FASEB journal : official publication of the Federation of American Societies for Experimental Biology", "date": "2023-06", "authors": "Zhang Yanni, Xi Qiulei, Zhong Ming, Jiang Yi, Zhuang Qiulin, Ding Zuoyou, Tan Shanjun, Wang Junjie, Liu Hao, Zhang Zhige, Zhou Ben, Wu Guohao", "evidence": [ { "database": "RefSeq", "id": "NP_689967", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_689967" } ], "reference": [ { "type": "PubMed", "id": "37219490", "url": "https://glygen.org/publication/PubMed/37219490" } ] } ], "pathway": [ { "id": "hsa:223117", "name": "", "url": "https://www.genome.jp/dbget-bin/get_linkdb?-t+pathway+hsa:223117", "resource": "KEGG Pathway" } ], "orthologs": [ { "uniprot_canonical_ac": "F1MAG8-1", "protein_name": "Semaphorin 3D", "gene_name": "Sema3d", "tax_id": 10116, "organism": "Rattus norvegicus", "sequence": { "sequence": "MNANKDENPRPRSQDLHLFHAGMMLIVTVLYLPVTETSKQNIPRLKLTYKDLLLSNTCIPFLGSSEGLDFQTLLLDEERGILLLGAKDHVFLLNLVDLNKNFKKIYWPAAKERVELCKLAGKDANTECANFIRVLQPYNKTHVYVCGTGAFHPLCGYIDLGANKEELIFKLDMQNLESGRLKCPFDPQQPFASVMTDEHLYSGTASDFLGKDTAFTRSLGLMQDHHYIRTDISEHYWLNGAKFIGTFPIPDTYNPDDDKIYFFFRESSQEGSTSDRSILSRVGRVCKNDVGGQRSLINKWTTFLKARLVCSIPGSDGADTHFDELQDIYLLPTRDERNPVVYGVFTTTSSIFKGSAVCVYSMADIRAVFNGPYAHKESADHRWVQYDGRIPYPRPGTCPSKTYDPLIKSTRDFPDDVISFIRRHPVMYKSVYPVAGAPTFKRINVDYRLTQIVVDHVVAEDGQYDVMFLGTDIGTVLKVVSISKEKWNMEEVVLEELQVFKHPTAILNMELSLKQQQLYVGSWDGLVQLSLHRCDTYGKACADCCLARDPYCAWDGNACSRYAPTSKRRARRQDVKYGDPITQCWDIEDSISHEAADEKVIFGIEFNSTFLECIPKSQQASVEWYIQRSGDEHREELKPDERIIKTDYGLLIRSLQKKDSGIYYCKAQEHTFIHTIVKLTLNVIENEQMENNQRAEYQEGQVKDLLAESRLRYKDYIQILSSPNFSLDQYCEQMWYREKRRQRNKGSAKWKHMQEMKKKRNRRHHRDLDELQRSVAT", "length": 777 }, "evidence": [ { "id": "45916854", "url": "http://www.informatics.jax.org/homology/45916854", "database": "MGI" }, { "id": "O95025", "url": "https://omabrowser.org/oma/group/O95025/", "database": "OMA" } ], "common_name": "Rat" }, { "uniprot_canonical_ac": "Q8BH34-1", "protein_name": "Semaphorin-3D", "gene_name": "Sema3d", "tax_id": 10090, "organism": "Mus musculus", "sequence": { "sequence": "MNVTKDENPRSRSQDLHLFHAWMMLIMTVLFLPVTETSKQNIPRLKLTYKDLLLSNTCIPFLGSSEGLDFQTLLLDEERGILLLGAKDHVFLLSLVDLNKNFKKIYWPAAKERVELCKLAGKDANAECANFIRVLQPYNKTHVYVCGTGAFHPLCGYIDLGANKEELIFKLDTHNLESGRLKCPFDPQQPFASVMTDEHLYSGTASDFLGKDTAFTRSLGLMQDHHSIRTDISEHHWLNGAKFIGTFPIPDTYNPDDDKIYFFFRESSQEGSTSDRSILSRVGRVCKNDVGGQRSLINKWTTFLKARLICSIPGSDGADTHFDELQDIYLLPTRDERNPVVYGVFTTTSSIFKGSAVCVYSMADIRAVFNGPYAHKESADHRWVQYDGRIPYPRPGTCPSKTYDPLIKSTRDFPDDVISFIRRHPVMYKSVYPVAGAPTFKRINVDYRLTQIVVDHVVAEDGQYDVMFLGTDIGTVLKVVSISKEKWNMEEVVLEELQVFKHPTAILNMELSLKQQQLYVGSWDGLVQLSLHRCDTYGKACADCCLARDPYCAWDGNACSRYAPTSKRRARRQDVKYGDPITQCWDIEDSISHETADEKVIFGIEFNSTFLECIPKSQQASVEWYIQRSGDEHREELKPDERIIKTDYGLLIRSLQKKDSGMYYCKAQEHTFIHTIVKLTLNVIENEQMENTQRAEYQEGQVKDLLAESRLRYKDYIQILSSPNFSLDQYCEQMWYKEKRRQRNKGSPKWKHMQEMKKKRNRRHHRDLDELQRSVAT", "length": 777 }, "evidence": [ { "id": "45916854", "url": "http://www.informatics.jax.org/homology/45916854", "database": "MGI" }, { "id": "O95025", "url": "https://omabrowser.org/oma/group/O95025/", "database": "OMA" } ], "common_name": "Mouse" } ], "go_annotation": { "categories": [ { "name": "Cellular Component", "total": 2, "go_terms": [ { "name": "membrane", "id": "GO:0016020", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0016020", "evidence": [ { "database": "UniProtKB", "id": "O95025", "url": "https://www.uniprot.org/uniprot/O95025" } ], "pmid": "" }, { "name": "extracellular space", "id": "GO:0005615", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0005615", "evidence": [ { "database": "UniProtKB", "id": "O95025", "url": "https://www.uniprot.org/uniprot/O95025" } ], "pmid": "" } ] }, { "name": "Molecular Function", "total": 2, "go_terms": [ { "name": "semaphorin receptor binding", "id": "GO:0030215", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0030215", "evidence": [ { "database": "UniProtKB", "id": "O95025", "url": "https://www.uniprot.org/uniprot/O95025" } ], "pmid": "" }, { "name": "chemorepellent activity", "id": "GO:0045499", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0045499", "evidence": [ { "database": "UniProtKB", "id": "O95025", "url": "https://www.uniprot.org/uniprot/O95025" } ], "pmid": "" } ] }, { "name": "Biological Process", "total": 6, "go_terms": [ { "name": "positive regulation of cell migration", "id": "GO:0030335", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0030335", "evidence": [ { "database": "UniProtKB", "id": "O95025", "url": "https://www.uniprot.org/uniprot/O95025" } ], "pmid": "" }, { "name": "semaphorin-plexin signaling pathway", "id": "GO:0071526", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0071526", "evidence": [ { "database": "UniProtKB", "id": "O95025", "url": "https://www.uniprot.org/uniprot/O95025" } ], "pmid": "" }, { "name": "neural crest cell migration", "id": "GO:0001755", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0001755", "evidence": [ { "database": "UniProtKB", "id": "O95025", "url": "https://www.uniprot.org/uniprot/O95025" } ], "pmid": "" }, { "name": "negative chemotaxis", "id": "GO:0050919", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0050919", "evidence": [ { "database": "UniProtKB", "id": "O95025", "url": "https://www.uniprot.org/uniprot/O95025" } ], "pmid": "" }, { "name": "axon guidance", "id": "GO:0007411", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0007411", "evidence": [ { "database": "UniProtKB", "id": "O95025", "url": "https://www.uniprot.org/uniprot/O95025" } ], "pmid": "" }, { "name": "negative regulation of axon extension involved in axon guidance", "id": "GO:0048843", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0048843", "evidence": [ { "database": "UniProtKB", "id": "O95025", "url": "https://www.uniprot.org/uniprot/O95025" } ], "pmid": "" } ] } ] }, "pro_annotation": [], "site_annotation": [ { "start_pos": 139, "end_pos": 141, "annotation": "n_glycosylation_sequon" }, { "start_pos": 607, "end_pos": 609, "annotation": "n_glycosylation_sequon" }, { "start_pos": 724, "end_pos": 726, "annotation": "n_glycosylation_sequon" } ], "ptm_annotation": [], "interactions": [], "reactions": [], "reaction_participants": [], "reaction_enzymes": [], "biomarkers": [], "synthesized_glycans": [], "cluster_types": [ { "name": "isoformset.uniprotkb", "label": "Isoforms" }, { "name": "homologset.mgi", "label": "MGI Homologs" }, { "name": "homologset.oma", "label": "OMA Homologs" } ], "sequence_features": { "n_linked_sites": [ 139, 607, 724 ], "o_linked_sites": [], "snv_sites": [ 26, 43, 139, 141, 231, 241, 272, 275, 294, 346, 353, 372, 400, 588, 590, 609, 653, 684, 726, 728, 760, 763 ], "glycation_sites": [], "phosphorylation_sites": [ 447 ], "sequon_annotation_sites": [ { "start_pos": 139, "end_pos": 141 }, { "start_pos": 607, "end_pos": 609 }, { "start_pos": 724, "end_pos": 726 } ] }, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 4 }, { "field": "total_sites", "count": 4 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 3 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_pos", "start_aa", "end_pos", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_glycans", 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