{ "bcoid": "GLY_000943", "title": "Pig Protein Site Annotation", "description": "The Pig Protein Site Annotation (UniProtKB) dataset contains human [taxid:1758] site annotations for ...", "filename": "pig_protein_site_annotation_uniprotkb.csv", "filetype": "csv", "categories": { "species": [ "Homo sapiens" ], "molecule": [ "Protein" ], "tag": [ "site annotation" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "A0A287AE97-1...", "PIGK..." ], [ "A0A287BAF3-1...", "ADSS1..." ] ], "headers": [ "uniprotkb_ca...", "gene_symbol..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "gene_symbol" }, { "type": "string", "label": "ann_type" }, { "type": "string", "label": "start_pos" }, { "type": "string", "label": "end_pos" }, { "type": "string", "label": "annotation" }, { "type": "string", "label": "ecoid" }, { "type": "string", "label": "ref_aa" }, { "type": "string", "label": "alt_aa" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" } ], [ "A0A287AE97-1", "PIGK", "Active_Site_Annotation", "206", "206", "Nucleophile", "ECO_0000256", "C", "", "protein_xref_uniprotkb", "A0A287BN24" ], [ "A0A287BAF3-1", "ADSS1", "Active_Site_Annotation", "43", "43", "Proton acceptor", "ECO_0000256", "D", "", "protein_xref_uniprotkb", "A0A5G2QKB5" ], [ "A0A287BAF3-1", "ADSS1", "Active_Site_Annotation", "71", "71", "Proton donor", "ECO_0000256", "H", "", "protein_xref_uniprotkb", "A0A5G2QKB5" ], [ "A0A5G2QM40-1", "CUX1", "Nucleotide_Binding_Annotation", "1352", "1411", "Homeobox", "ECO_0000256", "LKKPRVVLAPEEKEALKRAYQQKPYPSPKTIEELATQLNLKTSTVINWFHNYRSRIRREL", "", "protein_xref_uniprotkb", "A0A5G2QM40" ], [ "C0JPM4-1", "TIMP2", "Site_Annotation", "68", "68", "Involved in metalloproteinase-binding", "ECO_0000256", "K", "", "protein_xref_uniprotkb", "C0JPM4" ], [ "C0JPM4-1", "TIMP2", "Site_Annotation", "41", "41", "Involved in metalloproteinase-binding", "ECO_0000256", "N", "", "protein_xref_uniprotkb", "C0JPM4" ], [ "O97676-1", "SREBF1", "Site_Annotation", "490", "491", "Cleavage; by MBTPS2", "ECO_0000250", "LC", "", "protein_xref_uniprotkb", "O97676" ], [ "O97676-1", "SREBF1", "Site_Annotation", "460", "461", "Cleavage; by caspase-3 and caspase-7", "ECO_0000250", "DS", "", "protein_xref_uniprotkb", "O97676" ], [ "O97676-1", "SREBF1", "Site_Annotation", "530", "531", "Cleavage; by MBTPS1", "ECO_0000250", "LG", "", "protein_xref_uniprotkb", "O97676" ], [ "O97676-1", "SREBF1", "Modified_Residue_Annotation", "1060", "1060", "Phosphoserine", "ECO_0000250", "S", "", "protein_xref_uniprotkb", "O97676" ], [ "O97676-1", "SREBF1", "Modified_Residue_Annotation", "397", "397", "Phosphoserine; by AMPK", "ECO_0000250", "S", "", "protein_xref_uniprotkb", "O97676" ], [ "O97676-1", "SREBF1", "Modified_Residue_Annotation", "338", "338", "Phosphoserine; by SIK1", "ECO_0000250", "S", "", "protein_xref_uniprotkb", "O97676" ], [ "O97676-1", "SREBF1", "Modified_Residue_Annotation", "98", "98", "Phosphoserine", "ECO_0000250", "S", "", "protein_xref_uniprotkb", "O97676" ], [ "O97676-1", "SREBF1", "Modified_Residue_Annotation", "117", "117", "Phosphoserine", "ECO_0000250", "S", "", "protein_xref_uniprotkb", "O97676" ], [ "O97676-1", "SREBF1", "Modified_Residue_Annotation", "457", "457", "Phosphoserine", "ECO_0000250", "S", "", "protein_xref_uniprotkb", "O97676" ], [ "O97676-1", "SREBF1", "Modified_Residue_Annotation", "403", "403", "Phosphoserine; by SIK1", "ECO_0000250", "S", "", "protein_xref_uniprotkb", "O97676" ], [ "O97676-1", "SREBF1", "Modified_Residue_Annotation", "339", "339", "Phosphoserine; by SIK1", "ECO_0000250", "S", "", "protein_xref_uniprotkb", "O97676" ], [ "P01232-1", "LHB", "Glycosylation_Annotation", "33", "33", "N-linked (GlcNAc...) asparagine", "ECO_0000269", "N", "", "protein_xref_uniprotkb", "P01232" ], [ "P01232-1", "LHB", "Glycosylation_Annotation", "33", "33", "N-linked (GlcNAc...) asparagine", "ECO_0000269", "N", "", "protein_xref_pubmed", "4770795" ], [ "P01232-1", "LHB", "Modified_Residue_Annotation", "21", "21", "Blocked amino end (Ser)", "ECO_0000269", "S", "", "protein_xref_uniprotkb", "P01232" ], [ "P01232-1", "LHB", "Modified_Residue_Annotation", "21", "21", "Blocked amino end (Ser)", "ECO_0000269", "S", "", "protein_xref_pubmed", "4770795" ], [ "A0A286ZRC3-1", "CRAT", "Active_Site_Annotation", "462", "462", "Proton acceptor", "ECO_0000256", "L", "", "protein_xref_uniprotkb", "A0A5G2QG61" ], [ "P01238-1", "PRL", "Glycosylation_Annotation", "61", "61", "N-linked (GlcNAc...) asparagine; partial", "", "N", "", "protein_xref_uniprotkb", "P01238" ], [ "P01238-1", "PRL", "Modified_Residue_Annotation", "56", "56", "Phosphoserine", "ECO_0000250", "S", "", "protein_xref_uniprotkb", "P01238" ], [ "P01238-1", "PRL", "Modified_Residue_Annotation", "120", "120", "Phosphoserine", "ECO_0000250", "S", "", "protein_xref_uniprotkb", "P01238" ], [ "P01238-1", "PRL", "Modified_Residue_Annotation", "64", "64", "Phosphoserine", "ECO_0000250", "S", "", "protein_xref_uniprotkb", "P01238" ], [ "Q8MJS1-1", "IL12RB2", "Glycosylation_Annotation", "480", "480", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8MJS1" ], [ "Q8MJS1-1", "IL12RB2", "Glycosylation_Annotation", "48", "48", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8MJS1" ], [ "Q8MJS1-1", "IL12RB2", "Glycosylation_Annotation", "376", "376", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8MJS1" ], [ "Q8MJS1-1", "IL12RB2", "Glycosylation_Annotation", "166", "166", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8MJS1" ], [ "Q8MJS1-1", "IL12RB2", "Glycosylation_Annotation", "271", "271", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8MJS1" ], [ "Q8MJS1-1", "IL12RB2", "Glycosylation_Annotation", "347", "347", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8MJS1" ], [ "Q8MJS1-1", "IL12RB2", "Glycosylation_Annotation", "129", "129", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8MJS1" ], [ "Q8MJS1-1", "IL12RB2", "Modified_Residue_Annotation", "800", "800", "Phosphotyrosine", "ECO_0000250", "Y", "", "protein_xref_uniprotkb", "Q8MJS1" ], [ "C9K505-1", "CDK7", "Active_Site_Annotation", "103", "103", "Proton acceptor", "ECO_0000256", "K", "", "protein_xref_uniprotkb", "A0A8D1V2T2" ], [ "P81693-1", "ACP1", "Active_Site_Annotation", "130", "130", "Proton donor", "ECO_0000250", "D", "", "protein_xref_uniprotkb", "P81693" ], [ "P81693-1", "ACP1", "Active_Site_Annotation", "13", "13", "Nucleophile", "ECO_0000250", "C", "", "protein_xref_uniprotkb", "P81693" ], [ "P81693-1", "ACP1", "Modified_Residue_Annotation", "132", "132", "Phosphotyrosine", "ECO_0000250", "Y", "", "protein_xref_uniprotkb", "P81693" ], [ "P81693-1", "ACP1", "Modified_Residue_Annotation", "2", "2", "N-acetylalanine", "ECO_0000250", "A", "", "protein_xref_uniprotkb", "P81693" ], [ "P81693-1", "ACP1", "Modified_Residue_Annotation", "133", "133", "Phosphotyrosine", "ECO_0000250", "Y", "", "protein_xref_uniprotkb", "P81693" ], [ "A0A5G2R105-1", "AOX4", "Active_Site_Annotation", "1261", "1261", "Proton acceptor", "ECO_0000256", "A", "", "protein_xref_uniprotkb", "A0A287BSQ9" ], [ "A0A287BF76-1", "HOXB9", "Nucleotide_Binding_Annotation", "185", "244", "Homeobox", "ECO_0000256", "SRKKRCPYTKYQTLELEKEFLFNMYLTRDRRHEVARLLNLSERQVKIWFQNRRMKMKKMN", "", "protein_xref_uniprotkb", "A0A287BF76" ], [ "A0A5G2Q9S8-1", "TXN", "Active_Site_Annotation", "35", "35", "Nucleophile", "ECO_0000256", "T", "", "protein_xref_uniprotkb", "A0A5G2QTF5" ], [ "A0A5G2Q9S8-1", "TXN", "Active_Site_Annotation", "32", "32", "Nucleophile", "ECO_0000256", "V", "", "protein_xref_uniprotkb", "A0A5G2QTF5" ], [ "A0A5G2Q9S8-1", "TXN", "Site_Annotation", "34", "34", "Contributes to redox 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[ "I3LU85-1", "ACHE", "Active_Site_Annotation", "233", "233", "Acyl-ester intermediate", "ECO_0000256", "S", "", "protein_xref_uniprotkb", "I3LU85" ], [ "A0A480VNP1-1", "PRKCZ", "Active_Site_Annotation", "413", "413", "Proton acceptor", "ECO_0000256", "G", "", "protein_xref_uniprotkb", "I3LU84" ], [ "A0A287BS41-1", "TGFB2", "Disulfide_Bond_Annotation", "408", "408", "Interchain", "ECO_0000256", "I", "", "protein_xref_uniprotkb", "A0A286ZV08" ], [ "F1RMZ4-1", "CUX2", "Nucleotide_Binding_Annotation", "1177", "1236", "Homeobox", "ECO_0000256", "KPRVVLAPEEKEALRKAYQLEPYPSQQTIELLSFQLNLKTNTVINWFHNYRSRMRREMLV", "", "protein_xref_uniprotkb", "A0A8W4FD43" ], [ "A0A173G6H0-1", "SEPTIN5", "Site_Annotation", "161", "161", "Important for dimerization", "ECO_0000256", "S", "", "protein_xref_uniprotkb", "A0A287A666" ], [ "A0A286ZSW9-1", "TCF7L2", "Nucleotide_Binding_Annotation", "375", "443", "HMG box", "ECO_0000256", "DVSSLHSAKHQDSKKEEEKKKPHIKKPLNAFMLYMKEMRAKVVAECTLKESAAINQILGRRWHALSREE", "", "protein_xref_uniprotkb", "A0A287A661" ], [ "A0A8W4FL06-1", "LIPI", "Active_Site_Annotation", "142", "142", "Nucleophile", "ECO_0000256", "N", "", "protein_xref_uniprotkb", "A0A286ZNN2" ], [ "A0A8W4FL06-1", "LIPI", "Active_Site_Annotation", "166", "166", "Charge relay system", "ECO_0000256", "L", "", "protein_xref_uniprotkb", "A0A286ZNN2" ], [ "A0A8W4FL06-1", "LIPI", "Active_Site_Annotation", "236", "236", "Charge relay system", "ECO_0000256", "I", "", "protein_xref_uniprotkb", "A0A286ZNN2" ], [ "Q2HYU2-1", "PFKM", "Active_Site_Annotation", "166", "166", "Proton acceptor", "ECO_0000255", "D", "", "protein_xref_uniprotkb", "Q2HYU2" ], [ "Q2HYU2-1", "PFKM", "Binding_Site_Annotation", "629", "629", "in other chain", "ECO_0000255", "E", "", "protein_xref_uniprotkb", "Q2HYU2" ], [ "Q2HYU2-1", "PFKM", "Binding_Site_Annotation", "208", "210", "in other chain", "ECO_0000255", "MGR", "", "protein_xref_uniprotkb", "Q2HYU2" ], [ "Q2HYU2-1", "PFKM", "Binding_Site_Annotation", "573", "575", "in other chain", "ECO_0000255", "MGG", "", "protein_xref_uniprotkb", "Q2HYU2" ], [ "Q2HYU2-1", "PFKM", "Binding_Site_Annotation", "298", "301", "in other chain", "ECO_0000255", "HVQR", "", "protein_xref_uniprotkb", "Q2HYU2" ], [ "Q2HYU2-1", "PFKM", "Binding_Site_Annotation", "528", "532", "in other chain", "ECO_0000255", "TVSNN", "", "protein_xref_uniprotkb", "Q2HYU2" ], [ "Q2HYU2-1", "PFKM", "Binding_Site_Annotation", "264", "264", "in other chain", "ECO_0000255", "E", "", "protein_xref_uniprotkb", "Q2HYU2" ], [ "Q2HYU2-1", "PFKM", "Binding_Site_Annotation", "164", "166", "in other chain", "ECO_0000255", "SID", "", "protein_xref_uniprotkb", "Q2HYU2" ], [ "Q2HYU2-1", "PFKM", "Binding_Site_Annotation", "471", "471", "in other chain", "ECO_0000255", "R", "", "protein_xref_uniprotkb", "Q2HYU2" ], [ "Q2HYU2-1", "PFKM", "Binding_Site_Annotation", "735", "735", "in other chain", "ECO_0000255", "R", "", "protein_xref_uniprotkb", "Q2HYU2" ], [ "Q2HYU2-1", "PFKM", "Binding_Site_Annotation", "661", "664", "in other chain", "ECO_0000255", "HMQQ", "", "protein_xref_uniprotkb", "Q2HYU2" ], [ "Q2HYU2-1", "PFKM", "Glycosylation_Annotation", "530", "530", "O-linked (GlcNAc) serine", "", "S", "", "protein_xref_uniprotkb", "Q2HYU2" ], [ "Q2HYU2-1", "PFKM", "Modified_Residue_Annotation", "377", "377", "Phosphoserine", "ECO_0000250", "S", "", "protein_xref_uniprotkb", "Q2HYU2" ], [ "Q2HYU2-1", "PFKM", "Modified_Residue_Annotation", "557", "557", "N6-(2-hydroxyisobutyryl)lysine", "ECO_0000250", "K", "", "protein_xref_uniprotkb", "Q2HYU2" ], [ "Q2HYU2-1", "PFKM", "Modified_Residue_Annotation", "775", "775", "Phosphoserine", "ECO_0000250", "S", "", "protein_xref_uniprotkb", "Q2HYU2" ], [ "Q2HYU2-1", "PFKM", "Modified_Residue_Annotation", "2", "2", "N-acetylthreonine", "ECO_0000250", "T", "", "protein_xref_uniprotkb", "Q2HYU2" ], [ "Q2HYU2-1", "PFKM", "Modified_Residue_Annotation", "667", "667", "Phosphoserine", "ECO_0000250", "S", "", "protein_xref_uniprotkb", "Q2HYU2" ], [ "F1RL75-1", "PDGFRB", "Active_Site_Annotation", "823", "823", "Proton acceptor", "ECO_0000256", "S", "", "protein_xref_uniprotkb", "A0A8W4FFG6" ], [ "A0A286ZLI2-1", "JAK1", "Active_Site_Annotation", "959", "959", "Proton acceptor", "ECO_0000256", "L", "", "protein_xref_uniprotkb", "A0A8W4F8J4" ], [ "A0A287AUE4-1", "UBE2K", "Active_Site_Annotation", "92", "92", "Glycyl thioester intermediate", "ECO_0000256", "C", "", "protein_xref_uniprotkb", "A0A287AUE4" ], [ "A0A287B1N9-1", "RBFOX2", "Site_Annotation", "188", "188", "Interaction with RNA", "ECO_0000256", "I", "", "protein_xref_uniprotkb", "A0A286ZMC4" ], [ "A0A287B1N9-1", "RBFOX2", "Site_Annotation", "145", "145", "Interaction with RNA", "ECO_0000256", "P", "", "protein_xref_uniprotkb", "A0A286ZMC4" ], [ "A0A287B1N9-1", "RBFOX2", "Site_Annotation", "120", "120", "Interaction with RNA", "ECO_0000256", "A", "", "protein_xref_uniprotkb", "A0A286ZMC4" ], [ "A0A287B1N9-1", "RBFOX2", "Site_Annotation", "112", "112", "Interaction with RNA", "ECO_0000256", "G", "", "protein_xref_uniprotkb", "A0A286ZMC4" ] ] }, "readme": "Name\n - Pig Protein Site Annotation\n\nVersion\n - v-2.4.1\n\nCreated on\n - 2019-12-01T15:29:48.229274\n\nModified on\n - 2024-02-28T17:57:21\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu], Urnisha Bhuiyan [sbhuiyan28@email.gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu]\n\nAuthors\n - Maria Martin [martin@ebi.ac.uk], Preethi Vasudev [pvasudev@ebi.ac.uk]\n\nChecksum\n - \n\nUsability Domain\n - The Pig Protein Site Annotation (UniProtKB) dataset contains human [taxid:1758] site annotations for UniProtKB canonical accessions. The dataset contains information about UniProtKB annotations with their amino acid range. The dataset is derived form 2019-09 UniprotKB release. If you use this dataset please give proper attribution to UniProtKB and GlyGen\n\nDescription Domain\n Keywords\n - site annotation\n - amino acid range\n - UniProtKB\n\n Pipeline Steps\n - Step-1: The script extracts the site annotation triples from the triplestore for the UniProtKB canonical sequnces asnd extracts as a dataset in a csv format\n\nExecution Domain\n Scripts - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/make-protein-dataset.py\n\n\n Software Prerequisites\n Name: Python\n Version: 2.7.5\n URI: https://www.python.org/download/releases/2.7.5/\n\nI/O Domain\n Input Subdomain\n Name: pig_protein_masterlist.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/pig_protein_masterlist.csv\n Name: uniprot-proteome-sus_scrofa.nt\n URI: https:/data.glygen.org/ln2downloads/ebi/2024_02_19/uniprot-proteome-sus_scrofa.nt\n Output Subdomain\n Name: pig_protein_site_annotation_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/pig_protein_site_annotation_uniprotkb.csv\n Name: pig_protein_site_annotation_uniprotkb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/pig_protein_site_annotation_uniprotkb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"2380\"\n Name: \"gene_symbol\"\n Description: \"\"Official gene name/symbol assigned to the gene. Human gene names/symbols are approved by the HUGO Gene Nomenclature Committee (HGNC)\"\n Unique Values: \"2176\"\n Name: \"ann_type\"\n Description: \"Annotation Type\"\n Unique Values: \"9\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"1404\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"1409\"\n Name: \"annotation\"\n Description: \"Function annotation from UniProtKB|RefSeq database\"\n Unique Values: \"821\"\n Name: \"ecoid\"\n Description: \"Evidence & Conclusion Ontology (ECO) identifier\"\n Unique Values: \"7\"\n Name: \"ref_aa\"\n Description: \"Reference amino acid residue\"\n Unique Values: \"716\"\n Name: \"alt_aa\"\n Description: \"Altered amino acid residue\"\n Unique Values: \"28\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"2\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"3921\"", "downloadurl": "/ln2data/releases/data/v-2.4.1/reviewed/pig_protein_site_annotation_uniprotkb.csv" }