{ "bcoid": "GLY_000272", "title": "Rat N-Glycosylation Sequon", "description": "The Rat N-Glycosylation Sequon dataset contains N-glycosylation sequon or motif or consensus sequence ...", "filename": "rat_protein_glycosylation_motifs.csv", "filetype": "csv", "categories": { "species": "Rattus norvegicus", "molecule": "Protein", "tags": "N-Glycosylation Sequon", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "D3ZB44-1...", "93..." ], [ "D3ZB44-1...", "112..." ] ], "headers": [ "uniprotkb_ca...", "start_pos..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "start_pos" }, { "type": "string", "label": "end_pos" }, { "type": "string", "label": "motif" } ], [ "D3ZB44-1", "93", "95", "NRT" ], [ "D3ZB44-1", "112", "114", "NYS" ], [ "D3ZB44-1", "201", "203", "NGS" ], [ "D3ZB44-1", "389", "391", "NLS" ], [ "D3ZB44-1", "473", "475", "NLT" ], [ "D3ZXJ3-1", "395", "397", "NHT" ], [ "Q64627-1", "120", "122", "NVT" ], [ "Q64627-1", "135", "137", "NWS" ], [ "Q64627-1", "302", "304", "NRT" ], [ "Q64627-1", "311", "313", "NQT" ], [ "D3ZB48-1", "671", "673", "NKS" ], [ "D3ZB48-1", "717", "719", "NLS" ], [ "Q5RJZ1-1", "128", "130", "NTS" ], [ "Q5RJZ1-1", "200", "202", "NGS" ], [ "Q04462-1", "186", "188", "NVT" ], [ "Q04462-1", "345", "347", "NVT" ], [ "Q04462-1", "476", "478", "NWS" ], [ "Q04462-1", "664", "666", "NRS" ], [ "Q04462-1", "805", "807", "NQS" ], [ "Q04462-1", "955", "957", "NAT" ], [ "Q04462-1", "1126", "1128", "NLT" ], [ "P11980-1", "75", "77", "NFS" ], [ "Q9WVK3-1", "131", "133", "NLT" ], [ "Q9WVK3-1", "180", "182", "NLT" ], [ "Q9WVK3-1", "271", "273", "NFT" ], [ "A0A0G2JVG6-1", "394", "396", "NYT" ], [ "A0A0G2JVG6-1", "506", "508", "NYT" ], [ "A0A0G2JVG6-1", "562", "564", "NFT" ], [ "P30938-1", "13", "15", "NAS" ], [ "P30938-1", "23", "25", "NWS" ], [ "P30938-1", "186", "188", "NLS" ], [ "A0A0G2JVG8-1", "5", "7", "NQS" ], [ "A0A0G2JVG8-1", "265", "267", "NNT" ], [ "Q07969-1", "79", "81", "NSS" ], [ "Q07969-1", "102", "104", "NIT" ], [ "Q07969-1", "134", "136", "NFT" ], [ "Q07969-1", "205", "207", "NNT" ], [ "Q07969-1", "220", "222", "NIS" ], [ "Q07969-1", "235", "237", "NLS" ], [ "Q07969-1", "247", "249", "NGT" ], [ "Q07969-1", "321", "323", "NCT" ], [ "Q07969-1", "417", "419", "NET" ], [ "A0A096MJY8-1", "2", "4", "NRS" ], [ "A0A096MJY8-1", "121", "123", "NMS" ], [ "A0A096MJY8-1", "250", "252", "NAT" ], [ "A0A096MJY4-1", "49", "51", "NST" ], [ "A0A096MJY4-1", "283", "285", "NNS" ], [ "A0A096MJY4-1", "379", "381", "NLS" ], [ "B2GV58-1", "33", "35", "NST" ], [ "B2GV58-1", "254", "256", "NDS" ], [ "B2GV58-1", "372", "374", "NIS" ], [ "A0A0G2JTB2-1", "84", "86", "NKS" ], [ "A0A0G2JTB2-1", "455", "457", "NMS" ], [ "A0A0G2JTB2-1", "510", "512", "NES" ], [ "A0A0G2JTB2-1", "521", "523", "NLT" ], [ "A0A0G2JTB2-1", "564", "566", "NKT" ], [ "A0A0G2KA92-1", "67", "69", "NSS" ], [ "A0A0G2KA92-1", "126", "128", "NRS" ], [ "A0A0G2KA92-1", "242", "244", "NVS" ], [ "A0A0G2KA92-1", "461", "463", "NNS" ], [ "A0A0G2KA92-1", "966", "968", "NNS" ], [ "A0A0G2KA92-1", "1096", "1098", "NDS" ], [ "A0A0G2KA92-1", "1208", "1210", "NAS" ], [ "A0A0G2KA92-1", "1705", "1707", "NMS" ], [ "A0A096MJY2-1", "16", "18", "NKS" ], [ "A0A096MJY2-1", "222", "224", "NAS" ], [ "A0A096MJY2-1", "257", "259", "NST" ], [ "F7ES73-1", "216", "218", "NQT" ], [ "F7ES73-1", "480", "482", "NNS" ], [ "Q63358-1", "291", "293", "NNS" ], [ "Q63358-1", "292", "294", "NSS" ], [ "Q63358-1", "413", "415", "NVT" ], [ "Q63358-1", "1166", "1168", "NST" ], [ "Q63358-1", "1256", "1258", "NST" ], [ "Q63358-1", "1565", "1567", "NKT" ], [ "Q63358-1", "1701", "1703", "NRT" ], [ "Q63358-1", "1778", "1780", "NHT" ], [ "P30937-1", "21", "23", "NAS" ], [ "P30936-1", "18", "20", "NAS" ], [ "P30936-1", "31", "33", "NAS" ], [ "O35158-1", "99", "101", "NNS" ], [ "O35158-1", "179", "181", "NVS" ], [ "O35158-1", "286", "288", "NYS" ], [ "O35158-1", "293", "295", "NNS" ] ] }, "readme": "Name\n - Rat N-Glycosylation Sequon\n\nVersion\n - 1.11.2\n\nCreated on\n - 2019-09-06T14:06:38.998256\n\nModified on\n - 2020-04-10T12:09:02.588363\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Xavier Holmes [xavierh@email.gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Amanda Bell [amandab2140@gwu.edu], Jonathon Keeney [keeneyjg@gwu.edu], Millicent Quartey [mquartey@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 Rat N-Glycosylation Sequon dataset contains N-glycosylation sequon or motif or consensus sequence for rat [taxid:10116] UniProtKB canonical sequences identified by the script. The script identifies the N-glycosylation sequon pattern - Asn-X-Ser/Thr , where X is any amino acid except proline (Pro) for UniProtKb accessions. If you use this dataset please provide proper attribution to GlyGen. The dataset is derived form 2019-09 UniprotKB release.\n\nDescription Domain\n Keywords\n - n-glycosylation sequon\n - NXS/T\n - n-glycosylation motif\n - n-glycosylation consensus sequence\n\n Pipeline Steps\n - Step-1: The script uses the PS Scan tool (accession- PS00001) from ProSite to extracts the N-glycosylation pattern/sequon/motif N-{P}-[ST]-{P} where P is not a proline from the UniProtKB canonical sequences. More info - https://prosite.expasy.org/PDOC00001, https://prosite.expasy.org/PS00001 and extracts as a csv.\n\nExecution Domain\n Scripts - https://github.com/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/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: rat_protein_canonicalsequences.fasta\n URI: https://data.glygen.org//ln2data/releases/data/v-1.11.2/reviewed/rat_protein_canonicalsequences.fasta\n Output Subdomain\n Name: rat_protein_glycosylation_motifs.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.12.1/reviewed/rat_protein_glycosylation_motifs.csv\n Name: rat_protein_glycosylation_motifs.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.12.1/reviewed/rat_protein_glycosylation_motifs.stat.csv", "downloadurl": "/ln2data/releases/data/v-1.12.1/reviewed/rat_protein_glycosylation_motifs.csv" }