{ "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" ], [ "M0R9X4-1", "37", "39", "NRS" ], [ "M0R9X4-1", "135", "137", "NSS" ], [ "M0R9X4-1", "187", "189", "NVS" ], [ "M0R9X4-1", "340", "342", "NSS" ], [ "M0R9X4-1", "401", "403", "NTS" ], [ "M0R9X4-1", "415", "417", "NLS" ], [ "M0R9X4-1", "419", "421", "NET" ], [ "M0R9X4-1", "422", "424", "NTT" ], [ "M0R9X4-1", "428", "430", "NVS" ], [ "M0R9X4-1", "694", "696", "NRT" ], [ "D3ZB41-1", "292", "294", "NAT" ], [ "D3ZB41-1", "384", "386", "NSS" ], [ "D3ZB41-1", "486", "488", "NTS" ], [ "D3ZB41-1", "711", "713", "NSS" ], [ "P09812-1", "24", "26", "NVS" ], [ "P09812-1", "275", "277", "NIS" ], [ "P09812-1", "339", "341", "NDT" ], [ "P09812-1", "377", "379", "NHT" ], [ "P09812-1", "482", "484", "NKT" ], [ "A0A8I6ASB1-1", "29", "31", "NYS" ], [ "A0A8I6ASB1-1", "268", "270", "NGS" ], [ "A0A8I6ASB1-1", "475", "477", "NLS" ], [ "A0A8I6ASB1-1", "489", "491", "NSS" ], [ "A0A8I6AX65-1", "675", "677", "NKS" ], [ "A0A8I6AX65-1", "721", "723", "NLS" ], [ "A0A8I6A5H0-1", "68", "70", "NIS" ], [ "A0A8I6A5H0-1", "109", "111", "NIS" ], [ "A0A8I6A5H0-1", "121", "123", "NLT" ], [ "A0A8I6A5H0-1", "170", "172", "NDS" ], [ "A0A8I6A5H0-1", "182", "184", "NGS" ], [ "A0A8I6A5H0-1", "199", "201", "NKT" ], [ "A0A8I6A5H0-1", "232", "234", "NSS" ], [ "A0A8I6A5H0-1", "284", "286", "NTS" ], [ "A0A8I6A5H0-1", "364", "366", "NVT" ], [ "A0A8I6A5H0-1", "413", "415", "NVS" ], [ "A0A8I6A5H0-1", "424", "426", "NFT" ], [ "A0A8I6A5H0-1", "435", "437", "NSS" ], [ "A0A8I6A5H0-1", "679", "681", "NFT" ], [ "Q5RJZ1-1", "128", "130", "NTS" ], [ "Q5RJZ1-1", "200", "202", "NGS" ], [ "A0A0G2K1R8-1", "51", "53", "NHS" ], [ "A0A0G2K1R8-1", "132", "134", "NST" ], [ "A0A0G2K1R8-1", "665", "667", "NGS" ], [ "A0A0G2K1R8-1", "687", "689", "NFT" ], [ "P11980-1", "75", "77", "NFS" ], [ "Q9WVK3-1", "131", "133", "NLT" ], [ "Q9WVK3-1", "180", "182", "NLT" ], [ "Q9WVK3-1", "271", "273", "NFT" ], [ "A0A0G2JVG6-1", "468", "470", "NYT" ], [ "A0A0G2JVG6-1", "580", "582", "NYT" ], [ "A0A0G2JVG6-1", "636", "638", "NFT" ], [ "P30938-1", "13", "15", "NAS" ], [ "P30938-1", "23", "25", "NWS" ], [ "P30938-1", "186", "188", "NLS" ], [ "P32301-1", "63", "65", "NRT" ], [ "P32301-1", "82", "84", "NVS" ], [ "P32301-1", "115", "117", "NSS" ], [ "P33578-1", "212", "214", "NLS" ], [ "A0A8I6AEC8-1", "156", "158", "NDS" ], [ "A0A8I6AEC8-1", "550", "552", "NTS" ], [ "A0A8I6AEC8-1", "810", "812", "NNS" ], [ "A0A8I6AEC8-1", "1317", "1319", "NCS" ], [ "A0A8I6AEC8-1", "1696", "1698", "NFS" ], [ "A0A8I6AEC8-1", "1994", "1996", "NET" ], [ "A0A8I6AEC8-1", "2201", "2203", "NYS" ], [ "A0A8I6GKT2-1", "133", "135", "NIS" ], [ "A0A8I6A2G6-1", "91", "93", "NNS" ], [ "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" ], [ "Q5XI22-1", "121", "123", "NMS" ], [ "Q5XI22-1", "250", "252", "NAS" ], [ "A0A096MJY4-1", "49", "51", "NST" ] ] }, "readme": "Name\n - Rat N-Glycosylation Sequon\n\nVersion\n - v-2.0.3\n\nCreated on\n - 2019-09-06T14:06:38.998256\n\nModified on\n - 2022-09-26T09:04:47.915182\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/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: rat_protein_canonicalsequences.fasta\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/rat_protein_canonicalsequences.fasta\n Name: prosite.dat\n URI: /data/shared/glyds/downloads/prosite/prosite.dat\n Output Subdomain\n Name: rat_protein_glycosylation_motifs.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/rat_protein_glycosylation_motifs.csv\n Name: rat_protein_glycosylation_motifs.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/rat_protein_glycosylation_motifs.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"17290\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"3639\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"3639\"\n Name: \"motif\"\n Description: \"Glycan motif\"\n Unique Values: \"39\"", "downloadurl": "/ln2data/releases/data/v-2.0.3/reviewed/rat_protein_glycosylation_motifs.csv" }