{ "bcoid": "GLY_000428", "title": "SARS-CoV2 N-Glycosylation Sequon", "description": "The SARS coronavirus (SARS-CoV-2 or 2019-nCov) N-Glycosylation Sequon dataset contains N-glycosylation ...", "filename": "sarscov2_protein_glycosylation_motifs.csv", "filetype": "csv", "categories": { "species": "SARS coronavirus (SARS-CoV-2 or 2019-nCoV)", "molecule": "Protein", "tags": "N-Glycosylation Sequon", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P0DTD1-1...", "348..." ], [ "P0DTD1-1...", "389..." ] ], "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" } ], [ "P0DTD1-1", "348", "350", "NLT" ], [ "P0DTD1-1", "389", "391", "NES" ], [ "P0DTD1-1", "434", "436", "NHT" ], [ "P0DTD1-1", "810", "812", "NNT" ], [ "P0DTD1-1", "840", "842", "NIT" ], [ "P0DTD1-1", "997", "999", "NQT" ], [ "P0DTD1-1", "1442", "1444", "NET" ], [ "P0DTD1-1", "1651", "1653", "NHT" ], [ "P0DTD1-1", "1719", "1721", "NKT" ], [ "P0DTD1-1", "1922", "1924", "NAS" ], [ "P0DTD1-1", "1996", "1998", "NAT" ], [ "P0DTD1-1", "2081", "2083", "NNS" ], [ "P0DTD1-1", "2102", "2104", "NSS" ], [ "P0DTD1-1", "2222", "2224", "NFS" ], [ "P0DTD1-1", "2272", "2274", "NST" ], [ "P0DTD1-1", "2275", "2277", "NVT" ], [ "P0DTD1-1", "2405", "2407", "NSS" ], [ "P0DTD1-1", "2498", "2500", "NGS" ], [ "P0DTD1-1", "2530", "2532", "NNT" ], [ "P0DTD1-1", "2623", "2625", "NVS" ], [ "P0DTD1-1", "2682", "2684", "NMT" ], [ "P0DTD1-1", "3382", "3384", "NGS" ], [ "P0DTD1-1", "3396", "3398", "NFT" ], [ "P0DTD1-1", "3405", "3407", "NGS" ], [ "P0DTD1-1", "3743", "3745", "NYS" ], [ "P0DTD1-1", "4173", "4175", "NTT" ], [ "P0DTD1-1", "4256", "4258", "NAT" ], [ "P0DTD1-1", "4263", "4265", "NST" ], [ "P0DTD1-1", "5159", "5161", "NST" ], [ "P0DTD1-1", "5303", "5305", "NTS" ], [ "P0DTD1-1", "5426", "5428", "NVT" ], [ "P0DTD1-1", "5581", "5583", "NIS" ], [ "P0DTD1-1", "5673", "5675", "NST" ], [ "P0DTD1-1", "5928", "5930", "NVT" ], [ "P0DTD1-1", "6054", "6056", "NNT" ], [ "P0DTD1-1", "6101", "6103", "NLS" ], [ "P0DTD1-1", "6480", "6482", "NNT" ], [ "P0DTD1-1", "6497", "6499", "NKT" ], [ "P0DTD1-1", "6936", "6938", "NVT" ], [ "P0DTD1-1", "6941", "6943", "NDS" ], [ "P0DTD1-1", "6996", "6998", "NAS" ], [ "A0A663DJA2-1", "36", "38", "NLT" ], [ "P0DTC6-1", "39", "41", "NLS" ], [ "P0DTC5-1", "5", "7", "NGT" ], [ "P0DTC4-1", "48", "50", "NVS" ], [ "P0DTC4-1", "66", "68", "NSS" ], [ "P0DTC2-1", "17", "19", "NLT" ], [ "P0DTC2-1", "61", "63", "NVT" ], [ "P0DTC2-1", "74", "76", "NGT" ], [ "P0DTC2-1", "122", "124", "NAT" ], [ "P0DTC2-1", "149", "151", "NKS" ], [ "P0DTC2-1", "165", "167", "NCT" ], [ "P0DTC2-1", "234", "236", "NIT" ], [ "P0DTC2-1", "282", "284", "NGT" ], [ "P0DTC2-1", "331", "333", "NIT" ], [ "P0DTC2-1", "343", "345", "NAT" ], [ "P0DTC2-1", "603", "605", "NTS" ], [ "P0DTC2-1", "616", "618", "NCT" ], [ "P0DTC2-1", "657", "659", "NNS" ], [ "P0DTC2-1", "709", "711", "NNS" ], [ "P0DTC2-1", "717", "719", "NFT" ], [ "P0DTC2-1", "801", "803", "NFS" ], [ "P0DTC2-1", "1074", "1076", "NFT" ], [ "P0DTC2-1", "1098", "1100", "NGT" ], [ "P0DTC2-1", "1134", "1136", "NNT" ], [ "P0DTC2-1", "1158", "1160", "NHT" ], [ "P0DTC2-1", "1173", "1175", "NAS" ], [ "P0DTC2-1", "1194", "1196", "NES" ], [ "P0DTC1-1", "348", "350", "NLT" ], [ "P0DTC1-1", "389", "391", "NES" ], [ "P0DTC1-1", "434", "436", "NHT" ], [ "P0DTC1-1", "810", "812", "NNT" ], [ "P0DTC1-1", "840", "842", "NIT" ], [ "P0DTC1-1", "997", "999", "NQT" ], [ "P0DTC1-1", "1442", "1444", "NET" ], [ "P0DTC1-1", "1651", "1653", "NHT" ], [ "P0DTC1-1", "1719", "1721", "NKT" ], [ "P0DTC1-1", "1922", "1924", "NAS" ], [ "P0DTC1-1", "1996", "1998", "NAT" ], [ "P0DTC1-1", "2081", "2083", "NNS" ], [ "P0DTC1-1", "2102", "2104", "NSS" ], [ "P0DTC1-1", "2222", "2224", "NFS" ], [ "P0DTC1-1", "2272", "2274", "NST" ], [ "P0DTC1-1", "2275", "2277", "NVT" ] ] }, "readme": "Name\n - SARS-CoV2 N-Glycosylation Sequon\n\nVersion\n - 1.5.23\n\nCreated on\n - 2020-04-03T11:46:41.584409\n\nModified on\n - 2020-04-10T12:26:05.361474\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@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 SARS coronavirus (SARS-CoV-2 or 2019-nCov) N-Glycosylation Sequon dataset contains N-glycosylation sequon or motif or consensus sequence for sarscov2 [taxid:2697049] 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. The dataset is derived form 2020_01 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: sarscov2_protein_canonicalsequences.fasta\n URI: https://data.glygen.org/ln2wwwdata/reviewed/sarscov2_protein_canonicalsequences.fasta\n Output Subdomain\n Name: sarscov2_protein_glycosylation_motifs.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/sarscov2_protein_glycosylation_motifs.csv\n Name: sarscov2_protein_glycosylation_motifs.stat.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/sarscov2_protein_glycosylation_motifs.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"Accession assigned to the protein isoform chosen to be the canonical sequence to which all positional annotation refers in UniProtKB database\"\n Unique Values: \"10\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"75\"\n Name: \"motif\"\n Description: \"Glycan motif\"\n Unique Values: \"29\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"75\"", "downloadurl": "/ln2data/releases/data/v-1.5.23/reviewed/sarscov2_protein_glycosylation_motifs.csv" }