{ "bcoid": "GLY_000716", "title": "Human O-Glucosylation Glycosylation Sites", "description": "The Human O-Gluc Glycosylation Sites contains human (taxid:9606) O-Glucosylation sites from OGLUT2 and ...", "filename_list": "human_proteoform_glycosylation_sites_o_gluc.csv", "filename": "human_proteoform_glycosylation_sites_o_gluc.csv", "filetype": "csv", "categories": { "species": [ "Homo sapiens" ], "molecule": [ "Proteoform" ], "tag": [ "O-Glucosylation Sites" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "O43897-1...", "596..." ], [ "O43897-1...", "751..." ] ], "headers": [ "uniprotkb_ca...", "glycosylatio..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "glycosylation_site_uniprotkb" }, { "type": "string", "label": "amino_acid" }, { "type": "string", "label": "saccharide" }, { "type": "string", "label": "glycosylation_type" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "src_xref_key" }, { "type": "string", "label": "src_xref_id" }, { "type": "string", "label": "glycosylation_subtype" }, { "type": "string", "label": "carb_name" }, { "type": "string", "label": "notes" }, { "type": "string", "label": "start_pos" }, { "type": "string", "label": "end_pos" }, { "type": "string", "label": "start_aa" }, { "type": "string", "label": "end_aa" }, { "type": "string", "label": "site_seq" } ], [ "O43897-1", "596", "Ser", "G71142DF", "O-linked", "protein_xref_prosite_prorule", "PRU00076", "protein_xref_data_submission", "GLY_000716", "O-glucosylation", "Glc", "Predicted using consensus sequence C3-x-N-T-x-G-S-(FY)-x-C4. Glycosylation by enzyme POGLUT2 and POGLUT3. ", "596", "596", "Ser", "Ser", "S" ], [ "O43897-1", "751", "Ser", "G71142DF", "O-linked", "protein_xref_prosite_prorule", "PRU00076", "protein_xref_data_submission", "GLY_000716", "O-glucosylation", "Glc", "Predicted using consensus sequence C3-x-N-T-x-G-S-(FY)-x-C4. Glycosylation by enzyme POGLUT2 and POGLUT3. ", "751", "751", "Ser", "Ser", "S" ] ] }, "readme": "Name\n - Human O-Glucosylation Glycosylation Sites\n\nVersion\n - v-2.7.1\n\nCreated on\n - 2023-02-27T21:41:28.559Z\n\nModified on\n - 2024-11-04T21:19:19.089Z\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Luke Johnson [luke.johnson@email.gwu.edu], Urnisha Bhuiyan [sbhuiyan28@email.gwu.edu], Cyrus Au-Yeung [cyruschauyeung@gwu.edu], Kate Warner [k.warner1@gwu.edu]\n\nAuthors\n - Daniel Williamson [daniel.williamson25@uga.edu], Daniel Williamson [daniel.williamson25@uga.edu], Robert S Haltiwanger [rhalti@uga.edu]\n\nChecksum\n - \n\nUsability Domain\n - The Human O-Gluc Glycosylation Sites contains human (taxid:9606) O-Glucosylation sites from OGLUT2 and POGLUT3 O - glucosylate multiple EGF repeats in fibrillin - 1, -2, and LTBP1 and promote secretion of fibrillin - 1 [PMID:34411563] (experimental) and based on the consensus sequence the other sites (predicted) were detected using Prosite Prorule. The GlyTouCan ID for O-Gluc is G71142DF and the consensus sequence for O-gluc glycosylation is C3-x-N-T-x-G-S-(FY)-x-C4. The enzymes for o-glucosylation is POGLUT2 and POGLUT3. The dataset also contains Glycosylation stoichiometry: The relative amount (percentage) of a glycoform based on peptide signal intensity determined by mass spectrometry.\n - The dataset is generated in the lab of Robert S Haltiwanger by Daniel Williamson.\n\nDescription Domain\n Keywords\n - O-Gluc\n - O-Glucosylation\n\n Pipeline Steps\n - Step-1: The script maps the UniProtKB accesions to the UniProtKB Canonical accessions and also checks the position and amino acid of O-Gluc modified residue against UniProtKB Canonical sequences.\n\nExecution Domain\n Scripts - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/make-proteoform-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: human_proteoform_glycosylation_sites_o-gluc.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.7.1/compiled/human_proteoform_glycosylation_sites_o-gluc.csv\n Name: sample_mapping.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.7.1/misc/sample_mapping.csv\n Name: cellosaurus.txt\n URI: https:/data.glygen.org/ln2downloads/cellosaurus/2024_09_05/cellosaurus.txt\n Output Subdomain\n Name: human_proteoform_glycosylation_sites_o_gluc.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.7.1/reviewed/human_proteoform_glycosylation_sites_o_gluc.csv\n Name: human_proteoform_glycosylation_sites_o_gluc.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.7.1/reviewed/human_proteoform_glycosylation_sites_o_gluc.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"55\"\n Name: \"glycosylation_site_uniprotkb\"\n Description: \"Site on the protein sequence of the UniProtKB entry where glycosylation is observed\"\n Unique Values: \"177\"\n Name: \"amino_acid\"\n Description: \"Three letter abbreviation code of the amino acid\"\n Unique Values: \"2\"\n Name: \"saccharide\"\n Description: \"Sugar\"\n Unique Values: \"1\"\n Name: \"glycosylation_type\"\n Description: \"Type of glycosylation (N/O/C/S linked glycosylation)\"\n Unique Values: \"1\"\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: \"3\"\n Name: \"src_xref_key\"\n Description: \"Source Xref key\"\n Unique Values: \"1\"\n Name: \"src_xref_id\"\n Description: \"Source X-ref ID\"\n Unique Values: \"1\"\n Name: \"glycosylation_subtype\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"carb_name\"\n Description: \"carbohydrate name\"\n Unique Values: \"1\"\n Name: \"notes\"\n Description: \"Notes\"\n Unique Values: \"11\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"177\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"177\"\n Name: \"start_aa\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"end_aa\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"site_seq\"\n Description: \"\"\n Unique Values: \"2\"", "downloadurl": "/ln2data/releases/data/v-2.7.1/reviewed/human_proteoform_glycosylation_sites_o_gluc.csv" }