{ "uniprot_canonical_ac": "O60292-1", "uniprot_ac": "O60292", "uniprot_id": "SI1L3_HUMAN", "mass": { "chemical_mass": 194610.0, "monoisotopic_mass": 194610.0 }, "refseq": { "ac": "NP_055888", "name": "signal-induced proliferation-associated 1-like protein 3", "summary": "This gene belongs to the signal induced proliferation associated 1 family of genes, which encode GTPase-activating proteins specific for the GTP-binding protein Rap1. Rap1 has been implicated in regulation of cell adhesion, cell polarity, and organization of the cytoskeleton. Like other members of the family, the protein encoded by this gene contains RapGAP and PDZ domains. In addition, this protein contains a C-terminal leucine zipper domain. This gene is proposed to function in epithelial cell morphogenesis and establishment or maintenance of polarity. Consistently, expression of the protein in cell culture showed localization to cell-cell borders in apical regions, and downregulation of the gene in 3D Caco2 cell culture resulted in abnormal cell polarity and morphogenesis. Allelic variants of this gene have been associated with congenital cataracts in humans. [provided by RefSeq, Feb 2016].", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_055888" }, "gene_names": [ { "name": "SIPA1L3", "resource": "UniProtKB", "type": "recommended", "url": "https://www.uniprot.org/uniprot/O60292", "id": "O60292" }, { "name": "CTRCT45; SPAL3; SPAR3", "resource": "RefSeq", "type": "synonym", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_055888", "id": "NP_055888" }, { "name": "KIAA0545", "resource": "UniProtKB", "type": "synonym", "url": "https://www.uniprot.org/uniprot/O60292", "id": "O60292" }, { "name": "SIPA1L3", "resource": "RefSeq", "type": "synonym", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_055888", "id": "NP_055888" }, { "name": "SPAL3", "resource": "UniProtKB", "type": "synonym", "url": "https://www.uniprot.org/uniprot/O60292", "id": "O60292" } ], "protein_names": [ { "name": "Signal-induced proliferation-associated 1-like protein 3", "resource": "UniProtKB", "type": "recommended", "url": "", "id": "O60292" }, { "name": "SIPA1-like protein 3; SPA-1-like protein 3; spine-associated RapGAP 3", "resource": "RefSeq", "type": "synonym", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_055888", "id": "NP_055888" }, { "name": "SIPA1-like protein 3", "resource": "UniProtKB", "type": "synonym", "url": "", "id": "O60292" }, { "name": "SPA-1-like protein 3", "resource": "UniProtKB", "type": "synonym", "url": "", "id": "O60292" }, { "name": "signal-induced proliferation-associated 1-like protein 3", "resource": "RefSeq", "type": "synonym", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_055888", "id": "NP_055888" } ], "function": [ { "annotation": "Abnormalities of SIPA1L3 contribute to lens and eye defects, and we identify a critical role for SIPA1L3 in epithelial cell morphogenesis, polarity, adhesion and cytoskeletal organization.", "evidence": [ { "database": "RefSeq", "id": "NP_055888", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_055888" }, { "database": "PubMed", "id": "26231217", "url": "https://glygen.org/publication/PubMed/26231217" } ] }, { "annotation": "Plays a critical role in epithelial cell morphogenesis, polarity, adhesion and cytoskeletal organization in the lens (PubMed:26231217).", "evidence": [ { "database": "UniProtKB", "id": "O60292", "url": "https://www.uniprot.org/uniprot/O60292#function" }, { "database": "PubMed", "id": "26231217", "url": "https://glygen.org/publication/PubMed/26231217" } ] }, { "annotation": "Smoking cessation benefited survival of LUAD patients with low methylation at cg02268510SIPA 1L3 . The results have implications for not only smoking cessation after diagnosis, but also possible methylation-specific drug targeting.", "evidence": [ { "database": "RefSeq", "id": "NP_055888", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_055888" }, { "database": "PubMed", "id": "30924596", "url": "https://glygen.org/publication/PubMed/30924596" } ] }, { "annotation": "This gene belongs to the signal induced proliferation associated 1 family of genes, which encode GTPase-activating proteins specific for the GTP-binding protein Rap1. Rap1 has been implicated in regulation of cell adhesion, cell polarity, and organization of the cytoskeleton. Like other members of the family, the protein encoded by this gene contains RapGAP and PDZ domains. In addition, this protein contains a C-terminal leucine zipper domain. This gene is proposed to function in epithelial cell morphogenesis and establishment or maintenance of polarity. Consistently, expression of the protein in cell culture showed localization to cell-cell borders in apical regions, and downregulation of the gene in 3D Caco2 cell culture resulted in abnormal cell polarity and morphogenesis. Allelic variants of this gene have been associated with congenital cataracts in humans. [provided by RefSeq, Feb 2016].", "evidence": [ { "database": "RefSeq", "id": "NP_055888", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_055888" } ] }, { "annotation": "Whole-exome sequencing identified a homozygous nonsense variant in SIPA1L3 in two sisters with congenital cataract.", "evidence": [ { "database": "RefSeq", "id": "NP_055888", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_055888" }, { "database": "PubMed", "id": "25804400", "url": "https://glygen.org/publication/PubMed/25804400" } ] } ], "disease": [ { "disease_id": "DOID:0110262", "recommended_name": { "id": "DOID:0110262", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:0110262", "name": "cataract 45", "description": "A cataract that has_material_basis_in homozygous mutation in the SIPA1L3 gene on chromosome 19q13." }, "synonyms": [ { "id": "DOID:0110262", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:0110262", "name": "CTRCT45", "description": "" }, { "id": "MONDO:0014799", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014799", "name": "cataract 45", "description": "Any early-onset non-syndromic cataract in which the cause of the disease is a mutation in the SIPA1L3 gene." }, { "id": "MONDO:0014799", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014799", "name": "CTRCT45", "description": "" }, { "id": "MONDO:0014799", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014799", "name": "SIPA1L3 early-onset non-syndromic cataract", "description": "" }, { "id": "MONDO:0014799", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014799", "name": "cataract 45", "description": "" }, { "id": "MONDO:0014799", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014799", "name": "cataract type 45", "description": "" }, { "id": "MONDO:0014799", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014799", "name": "early-onset non-syndromic cataract caused by mutation in SIPA1L3", "description": "" }, { "id": "MIM:616851", "resource": "MIM", "url": "https://www.omim.org/entry/616851", "name": "Cataract 45", "description": "Cataract 45" } ], "evidence": [ { "id": "616851", "database": "MIM", "url": "https://www.omim.org/entry/616851" } ] } ], "snv": [ { "evidence": [ { "id": "rs878889858", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs878889858" }, { "id": "rs878889858", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs878889858" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "start_pos": 1076, "end_pos": 1076, "sequence_org": "Y", "sequence_mut": "N", "comment": "Germline mutation passed 1 out of 1 filters: n-glyco-sequon-gain (YRS->NRS).", "chr_id": "19", "chr_pos": "38141266", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y1076", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs967687984", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs967687984" }, { "id": "rs967687984", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs967687984#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "start_pos": 1115, "end_pos": 1115, "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 out of 1 filters: n-glyco-sequon-gain (KQT->NQT).", "chr_id": "19", "chr_pos": "38141385", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1115", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "O60292", "database": "BioMuta", "url": "https://hive.biochemistry.gwu.edu/biomuta/proteinview/O60292" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "start_pos": 1196, "end_pos": 1196, "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (DGT->NGT).", "chr_id": "19", "chr_pos": "38152892", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D1196", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "adenocarcinoma of lung, susceptibility to", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "Nonsmall cell lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "alveolar cell carcinoma", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung neoplasm", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs763818612", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763818612" }, { "id": "rs763818612", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763818612" }, { "id": "rs763818612", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs763818612#frequency_tab" }, { "id": "rs763818612", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763818612" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "start_pos": 1202, "end_pos": 1202, "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 out of 1 filters: n-glyco-sequon-gain (DSS->NSS).", "chr_id": "19", "chr_pos": "38152910", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1202", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1254883541", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1254883541" }, { "id": "rs1254883541", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1254883541#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "start_pos": 1307, "end_pos": 1307, "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 out of 1 filters: n-glyco-sequon-gain (SDS->NDS).", "chr_id": "19", "chr_pos": "38164618", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1307", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs143141927", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143141927" }, { "id": "rs143141927", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143141927" }, { "id": "rs143141927", "database": "NCI-TCGA", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143141927" }, { "id": "rs143141927", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs143141927#frequency_tab" }, { "id": "rs143141927", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs143141927" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "start_pos": 1312, "end_pos": 1312, "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 out of 1 filters: n-glyco-sequon-gain (DTT->NTT).", "chr_id": "19", "chr_pos": "38164632", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1312", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "O60292", "database": "BioMuta", "url": "https://hive.biochemistry.gwu.edu/biomuta/proteinview/O60292" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "start_pos": 1460, "end_pos": 1460, "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (KRT->NRT).", "chr_id": "19", "chr_pos": "38182690", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "K1460", "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": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, 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"url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "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": 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{ "database": "Bgee", "id": "ENSG00000105738", "url": "https://bgee.org/?page=gene&gene_id=ENSG00000105738" } ] }, { "tissue": { "name": "Esophagus", "namespace": "UBERON", "id": "0001043", "url": "http://purl.obolibrary.org/obo/UBERON_0001043" }, "score": "74.39", "present": "MEDIUM", "evidence": [ { "database": "Bgee", "id": "ENSG00000105738", "url": "https://bgee.org/?page=gene&gene_id=ENSG00000105738" } ] }, { "tissue": { "name": "Rectum", "namespace": "UBERON", "id": "0001052", "url": "http://purl.obolibrary.org/obo/UBERON_0001052" }, "score": "89.29", "present": "HIGH", "evidence": [ { "database": "Bgee", "id": "ENSG00000105738", "url": "https://bgee.org/?page=gene&gene_id=ENSG00000105738" } ] }, { "tissue": { "name": "Colon", "namespace": "UBERON", "id": "0001155", "url": "http://purl.obolibrary.org/obo/UBERON_0001155" }, "score": "88.36", "present": "HIGH", "evidence": [ { "database": "Bgee", "id": "ENSG00000105738", "url": "https://bgee.org/?page=gene&gene_id=ENSG00000105738" 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{ "id": "DOID:1612", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed 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Male", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ] } ] }, { "significant": "No", "trend": "down", "name": "Thyroid cancer [DO disease name]", "url": "http://disease-ontology.org/term/DOID:1781", "evidence": [ { "database": "BioXpress", "id": "O60292", "url": "https://hive.biochemistry.gwu.edu/bioxpress/transcriptview/O60292" } ], "disease": [ { "disease_id": "DOID:1781", "recommended_name": { "id": "DOID:1781", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:1781", "name": "thyroid cancer", "description": "An endocrine gland cancer located in the thryoid gland located in the neck below the thyroid cartilage." }, "synonyms": [ { "id": "DOID:1781", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:1781", "name": "thyroid gland cancer", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", 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"https://hive.biochemistry.gwu.edu/bioxpress/transcriptview/O60292" } ], "disease": [ { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ] } ] }, { "significant": "Yes", "trend": "up", "name": "Liver cancer [DO disease name]", "url": "http://disease-ontology.org/term/DOID:3571", "evidence": [ { "database": "BioXpress", "id": "O60292", "url": "https://hive.biochemistry.gwu.edu/bioxpress/transcriptview/O60292" } ], "disease": [ { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:3571", 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"length": 1781, "header": "sp|O60292-1|SI1L3_HUMAN Isoform 1 of Signal-induced proliferation-associated 1-like protein 3 OS=Homo sapiens OX=9606 GN=SIPA1L3 PE=1 SV=3 CANONICAL=O60292-1" }, "locus": { "chromosome": "19", "start_pos": 38206237, "end_pos": 38081566, "strand": "-", "evidence": [ { "database": "Ensembl Transcript", "id": "ENST00000222345.11", "url": "https://www.ensembl.org/id/ENST00000222345.11" }, { "database": "Ensembl Peptide", "id": "ENSP00000222345.4", "url": "https://www.ensembl.org/id/ENSP00000222345.4" } ] } } ], "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": 385, "start_aa": "Thr", "end_pos": 385, "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr385", "evidence": [ { "id": "O60292", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O60292" }, { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" } ] } ], "phosphorylation": [ { "start_pos": 100, "end_pos": 100, "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O60292", "url": "https://www.uniprot.org/uniprot/O60292" } ], "site_lbl": "Ser100" }, { "start_pos": 1135, "end_pos": 1135, "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "phospho.ELM", "id": "O60292", "url": "http://phospho.elm.eu.org/byAccession/O60292.html" }, { "database": "iPTMnet", "id": "O60292", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O60292" }, { "database": "PubMed", "id": "18220336", "url": "https://glygen.org/publication/PubMed/18220336" } ], "site_lbl": "Ser1135" }, { "start_pos": 1364, "end_pos": 1364, "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O60292", "url": "https://www.uniprot.org/uniprot/O60292" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "O60292", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O60292" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "phospho.ELM", "id": "O60292", "url": "http://phospho.elm.eu.org/byAccession/O60292.html" }, { "database": "PubMed", "id": "18220336", "url": "https://glygen.org/publication/PubMed/18220336" } ], "site_lbl": "Ser1364" }, { "start_pos": 1387, "end_pos": 1387, "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "O60292", "url": "https://www.uniprot.org/uniprot/O60292" } ], "site_lbl": "Thr1387" }, { "start_pos": 146, "end_pos": 146, "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O60292", "url": "https://www.uniprot.org/uniprot/O60292" }, { "database": "iPTMnet", "id": "O60292", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O60292" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ], "site_lbl": "Ser146" }, { "start_pos": 1544, "end_pos": 1544, "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O60292", "url": "https://www.uniprot.org/uniprot/O60292" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "O60292", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O60292" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" }, { "database": "PubMed", "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995" }, { "database": "phospho.ELM", "id": "O60292", "url": "http://phospho.elm.eu.org/byAccession/O60292.html" } ], "site_lbl": "Ser1544" }, { "start_pos": 1547, "end_pos": 1547, "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O60292", "url": "https://www.uniprot.org/uniprot/O60292" } ], "site_lbl": "Ser1547" }, { "start_pos": 1619, "end_pos": 1619, "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O60292", "url": "https://www.uniprot.org/uniprot/O60292" } ], "site_lbl": "Ser1619" }, { "start_pos": 1622, "end_pos": 1622, "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O60292", "url": "https://www.uniprot.org/uniprot/O60292" } ], "site_lbl": "Ser1622" }, { "start_pos": 1677, "end_pos": 1677, "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O60292", "url": "https://www.uniprot.org/uniprot/O60292" } ], "site_lbl": "Ser1677" }, { "start_pos": 1699, "end_pos": 1699, "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "O60292", "url": "https://www.uniprot.org/uniprot/O60292" }, { "database": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" }, { "database": "iPTMnet", "id": "O60292", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O60292" } ], "site_lbl": "Thr1699" }, { "start_pos": 1703, "end_pos": 1703, "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "O60292", "url": "https://www.uniprot.org/uniprot/O60292" }, { "database": "iPTMnet", "id": "O60292", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O60292" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "phospho.ELM", "id": "O60292", "url": "http://phospho.elm.eu.org/byAccession/O60292.html" } ], "site_lbl": "Thr1703" }, { "start_pos": 1705, "end_pos": 1705, "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O60292", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O60292" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "phospho.ELM", "id": "O60292", "url": "http://phospho.elm.eu.org/byAccession/O60292.html" } ], "site_lbl": "Thr1705" }, { "start_pos": 171, "end_pos": 171, "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O60292", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O60292" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "phospho.ELM", "id": "O60292", "url": "http://phospho.elm.eu.org/byAccession/O60292.html" } ], "site_lbl": "Ser171" }, { "start_pos": 401, "end_pos": 401, "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O60292", "url": "https://www.uniprot.org/uniprot/O60292" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "iPTMnet", "id": "O60292", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O60292" } ], "site_lbl": "Ser401" } ], "glycation": [], "keywords": [ "glycoprotein", "glycoprotein_reported_with_glycan" ], "publication": [ { "title": "Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis.", "journal": "Journal of proteome research", "date": "2008", "authors": "Cantin GT, Yi W, Lu B, Park SK, Xu T, Lee JD, Yates JR 3rd", "evidence": [ { "database": "iPTMnet", "id": "O60292", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O60292" } ], "reference": [ { "type": "PubMed", "id": "18220336", "url": "https://glygen.org/publication/PubMed/18220336" } ] }, { "title": "Motif-specific sampling of phosphoproteomes.", "journal": "Journal of proteome research", "date": "2008", "authors": "Ruse CI, McClatchy DB, Lu B, Cociorva D, Motoyama A, Park SK, Yates JR 3rd", "evidence": [ { "database": "iPTMnet", "id": "O60292", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O60292" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "title": "A quantitative atlas of mitotic phosphorylation.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2008", "authors": "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "O60292", "url": "https://www.uniprot.org/uniprot/O60292" }, { "database": "iPTMnet", "id": "O60292", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O60292" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle.", "journal": "Molecular cell", "date": "2008", "authors": "Daub H, Olsen JV, Bairlein M, Gnad F, Oppermann FS, Korner R, Greff Z, Keri G, Stemmann O, Mann M", "evidence": [ { "database": "iPTMnet", "id": "O60292", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O60292" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "O60292", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O60292" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] }, { "title": "Lysine acetylation targets protein complexes and co-regulates major cellular functions.", "journal": "Science (New York, N.Y.)", "date": "2009", "authors": "Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther TC, Olsen JV, Mann M", "evidence": [ { "database": "UniProtKB", "id": "O60292", "url": "https://www.uniprot.org/uniprot/O60292" } ], "reference": [ { "type": "PubMed", "id": "19608861", "url": "https://glygen.org/publication/PubMed/19608861" } ] }, { "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": "O60292", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O60292" } ], "reference": [ { "type": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ] }, { "title": "Phosphorylation dynamics during early differentiation of human embryonic stem cells.", "journal": "Cell stem cell", "date": "2009", "authors": "Van Hoof D, Munoz J, Braam SR, Pinkse MW, Linding R, Heck AJ, Mummery CL, Krijgsveld J", "evidence": [ { "database": "iPTMnet", "id": "O60292", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O60292" } ], "reference": [ { "type": "PubMed", "id": "19664995", "url": "https://glygen.org/publication/PubMed/19664995" } ] }, { "title": "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions.", "journal": "Science signaling", "date": "2009", "authors": "Mayya V, Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK", "evidence": [ { "database": "UniProtKB", "id": "O60292", "url": "https://www.uniprot.org/uniprot/O60292" }, { "database": "iPTMnet", "id": "O60292", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O60292" } ], "reference": [ { "type": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" } ] }, { "title": "Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations.", "journal": "Nature", "date": "2012", "authors": "Pugh TJ, Weeraratne SD, Archer TC, Pomeranz Krummel DA, Auclair D, Bochicchio J, Carneiro MO, Carter SL, Cibulskis K, Erlich RL, Greulich H, Lawrence MS, Lennon NJ, McKenna A, Meldrim J, Ramos AH, Ross MG, Russ C, Shefler E, Sivachenko A, Sogoloff B, Stojanov P, Tamayo P, Mesirov JP, Amani V, Teider N, Sengupta S, Francois JP, Northcott PA, Taylor MD, Yu F, Crabtree GR, Kautzman AG, Gabriel SB, Getz G, Jager N, Jones DT, Lichter P, Pfister SM, Roberts TM, Meyerson M, Pomeroy SL, Cho YJ", "evidence": [ { "database": "dbSNP", "id": "rs1471945520", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1471945520" } ], "reference": [ { "type": "PubMed", "id": "22820256", "url": "https://glygen.org/publication/PubMed/22820256" } ] }, { "title": "Toward a comprehensive characterization of a human cancer cell phosphoproteome.", "journal": "Journal of proteome research", "date": "2013", "authors": "Zhou H, Di Palma S, Preisinger C, Peng M, Polat AN, Heck AJ, Mohammed S", "evidence": [ { "database": "UniProtKB", "id": "O60292", "url": "https://www.uniprot.org/uniprot/O60292" }, { "database": "iPTMnet", "id": "O60292", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O60292" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome.", "journal": "Journal of proteomics", "date": "2014", "authors": "Bian Y, Song C, Cheng K, Dong M, Wang F, Huang J, Sun D, Wang L, Ye M, Zou H", "evidence": [ { "database": "UniProtKB", "id": "O60292", "url": "https://www.uniprot.org/uniprot/O60292" }, { "database": "iPTMnet", "id": "O60292", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O60292" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] }, { "title": "SIPA1L3 identified by linkage analysis and whole-exome sequencing as a novel gene for autosomal recessive congenital cataract.", "journal": "Eur. J. Hum. Genet.", "date": "2015", "authors": "Evers C, Paramasivam N, Hinderhofer K, Fischer C, Granzow M, Schmidt-Bacher A, Eils R, Steinbeisser H, Schlesner M, Moog U", "evidence": [ { "database": "UniProtKB", "id": "O60292", "url": "https://www.uniprot.org/uniprot/O60292" }, { "database": "RefSeq", "id": "NP_055888", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_055888" } ], "reference": [ { "type": "PubMed", "id": "25804400", "url": "https://glygen.org/publication/PubMed/25804400" } ] }, { "title": "Mutations in SIPA1L3 cause eye defects through disruption of cell polarity and cytoskeleton organization.", "journal": "Human molecular genetics", "date": "2015", "authors": "Greenlees R, Mihelec M, Yousoof S, Speidel D, Wu SK, Rinkwitz S, Prokudin I, Perveen R, Cheng A, Ma A, Nash B, Gillespie R, Loebel DA, Clayton-Smith J, Lloyd IC, Grigg JR, Tam PP, Yap AS, Becker TS, Black GC, Semina E, Jamieson RV", "evidence": [ { "database": "UniProtKB", "id": "O60292", "url": 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