{ "bcoid": "GLY_000328", "title": "Rat Protein Site Annotation", "description": "The Rat Protein Site Annotation (UniProtKB) dataset contains rat [taxid:10116] site annotations for UniProtKB ...", "filename": "rat_protein_site_annotation_uniprotkb.csv", "filetype": "csv", "categories": { "species": "Rattus norvegicus", "molecule": "Protein", "tags": "site annotation", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "Q5RJZ1-1...", "Rtel1..." ], [ "Q5RJZ1-1...", "Rtel1..." ] ], "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" } ], [ "Q5RJZ1-1", "Rtel1", "Metal_Binding_Annotation", "145", "145", "Iron-sulfur (4Fe-4S)", "ECO_0000256", "C", "", "protein_xref_uniprotkb", "A0A0G2JVG0" ], [ "Q5RJZ1-1", "Rtel1", "Metal_Binding_Annotation", "145", "145", "Iron-sulfur (4Fe-4S)", "ECO_0000256", "C", "", "protein_xref_pubmed", "MF_03065" ], [ "Q5RJZ1-1", "Rtel1", "Metal_Binding_Annotation", "172", "172", "Iron-sulfur (4Fe-4S)", "ECO_0000256", "C", "", "protein_xref_uniprotkb", "A0A0G2JVG0" ], [ "Q5RJZ1-1", "Rtel1", "Metal_Binding_Annotation", "172", "172", "Iron-sulfur (4Fe-4S)", "ECO_0000256", "C", "", "protein_xref_pubmed", "MF_03065" ], [ "Q5RJZ1-1", "Rtel1", "Metal_Binding_Annotation", "207", "207", "Iron-sulfur (4Fe-4S)", "ECO_0000256", "C", "", "protein_xref_uniprotkb", "A0A0G2JVG0" ], [ "Q5RJZ1-1", "Rtel1", "Metal_Binding_Annotation", "207", "207", "Iron-sulfur (4Fe-4S)", "ECO_0000256", "C", "", "protein_xref_pubmed", "MF_03065" ], [ "Q5RJZ1-1", "Rtel1", "Metal_Binding_Annotation", "163", "163", "Iron-sulfur (4Fe-4S)", "ECO_0000256", "C", "", "protein_xref_uniprotkb", "A0A0G2JVG0" ], [ "Q5RJZ1-1", "Rtel1", "Metal_Binding_Annotation", "163", "163", "Iron-sulfur (4Fe-4S)", "ECO_0000256", "C", "", "protein_xref_pubmed", "MF_03065" ], [ "Q0HA29-1", "Nmnat2", "Binding_Site_Annotation", "24", "24", "ATP", "ECO_0000250", "H", "", "protein_xref_uniprotkb", "Q0HA29" ], [ "Q0HA29-1", "Nmnat2", "Binding_Site_Annotation", "24", "24", "ATP", "ECO_0000250", "H", "", "protein_xref_pubmed", "Q96T66" ], [ "Q0HA29-1", "Nmnat2", "NP_Binding_Annotation", "271", "274", "ATP", "ECO_0000250", "TKSR", "", "protein_xref_uniprotkb", "Q0HA29" ], [ "Q0HA29-1", "Nmnat2", "NP_Binding_Annotation", "271", "274", "ATP", "ECO_0000250", "TKSR", "", "protein_xref_pubmed", "Q96T66" ], [ "Q0HA29-1", "Nmnat2", "NP_Binding_Annotation", "200", "202", "ATP", "ECO_0000250", "GSD", "", "protein_xref_uniprotkb", "Q0HA29" ], [ "Q0HA29-1", "Nmnat2", "NP_Binding_Annotation", "200", "202", "ATP", "ECO_0000250", "GSD", "", "protein_xref_pubmed", "Q96T66" ], [ "Q0HA29-1", "Nmnat2", "NP_Binding_Annotation", "15", "17", "ATP", "ECO_0000250", "GSF", "", "protein_xref_uniprotkb", "Q0HA29" ], [ "Q0HA29-1", "Nmnat2", "NP_Binding_Annotation", "15", "17", "ATP", "ECO_0000250", "GSF", "", "protein_xref_pubmed", "Q96T66" ], [ "P30938-1", "Sstr5", "Glycosylation_Annotation", "23", "23", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "P30938" ], [ "P30938-1", "Sstr5", "Glycosylation_Annotation", "186", "186", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "P30938" ], [ "P30938-1", "Sstr5", "Glycosylation_Annotation", "13", "13", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "P30938" ], [ "Q07969-1", "Cd36", "Site_Annotation", "463", "463", "Critical for TLR4-TLR6 dimerization and signaling", "ECO_0000250", "Y", "", "protein_xref_uniprotkb", "Q07969" ], [ "Q07969-1", "Cd36", "Site_Annotation", "463", "463", "Critical for TLR4-TLR6 dimerization and signaling", "ECO_0000250", "Y", "", "protein_xref_pubmed", "P16671" ], [ "Q07969-1", "Cd36", "Glycosylation_Annotation", "220", "220", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q07969" ], [ "Q07969-1", "Cd36", "Glycosylation_Annotation", "134", "134", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q07969" ], [ "Q07969-1", "Cd36", "Glycosylation_Annotation", "79", "79", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q07969" ], [ "Q07969-1", "Cd36", "Glycosylation_Annotation", "321", "321", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q07969" ], [ "Q07969-1", "Cd36", "Glycosylation_Annotation", "235", "235", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q07969" ], [ "Q07969-1", "Cd36", "Glycosylation_Annotation", "205", "205", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q07969" ], [ "Q07969-1", "Cd36", "Glycosylation_Annotation", "247", "247", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q07969" ], [ "Q07969-1", "Cd36", "Glycosylation_Annotation", "102", "102", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q07969" ], [ "Q07969-1", "Cd36", "Glycosylation_Annotation", "417", "417", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q07969" ], [ "A0A096MJY8-1", "Acat2l1", "Active_Site_Annotation", "92", "92", "Acyl-thioester intermediate", "ECO_0000256", "C", "", "protein_xref_uniprotkb", "A0A096MJY8" ], [ "A0A096MJY8-1", "Acat2l1", "Active_Site_Annotation", "92", "92", "Acyl-thioester intermediate", "ECO_0000256", "C", "", "protein_xref_pubmed", "PIRSR000429-1" ], [ "A0A096MJY8-1", "Acat2l1", "Active_Site_Annotation", "353", "353", "Proton acceptor", "ECO_0000256", "H", "", "protein_xref_uniprotkb", "A0A096MJY8" ], [ "A0A096MJY8-1", "Acat2l1", "Active_Site_Annotation", "353", "353", "Proton acceptor", "ECO_0000256", "H", "", "protein_xref_pubmed", "PIRSR000429-1" ], [ "A0A096MJY8-1", "Acat2l1", "Active_Site_Annotation", "383", "383", "Proton acceptor", "ECO_0000256", "C", "", "protein_xref_uniprotkb", "A0A096MJY8" ], [ "A0A096MJY8-1", "Acat2l1", "Active_Site_Annotation", "383", "383", "Proton acceptor", "ECO_0000256", "C", "", "protein_xref_pubmed", "PIRSR000429-1" ], [ "A0A096MJY4-1", "Mef2c", "Site_Annotation", "432", "433", "Cleavage", "ECO_0000250", "DG", "", "protein_xref_uniprotkb", "A0A096MJY4" ], [ "A0A096MJY4-1", "Mef2c", "Site_Annotation", "432", "433", "Cleavage", "ECO_0000250", "DG", "", "protein_xref_pubmed", "Q06413" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "116", "116", "N6-acetyllysine", "ECO_0000250", "K", "", "protein_xref_uniprotkb", "A0A096MJY4" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "116", "116", "N6-acetyllysine", "ECO_0000250", "K", "", "protein_xref_pubmed", "Q06413" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "419", "419", "Phosphoserine; by MAPK7", "ECO_0000250", "S", "", "protein_xref_uniprotkb", "A0A096MJY4" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "419", "419", "Phosphoserine; by MAPK7", "ECO_0000250", "S", "", "protein_xref_pubmed", "Q06413" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "106", "106", "Phosphoserine", "ECO_0000250", "S", "", "protein_xref_uniprotkb", "A0A096MJY4" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "106", "106", "Phosphoserine", "ECO_0000250", "S", "", "protein_xref_pubmed", "Q8CFN5" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "396", "396", "Phosphoserine; by CDK5", "ECO_0000250", "S", "", "protein_xref_uniprotkb", "A0A096MJY4" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "396", "396", "Phosphoserine; by CDK5", "ECO_0000250", "S", "", "protein_xref_pubmed", "Q06413" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "228", "228", "Phosphoserine", "ECO_0000250", "S", "", "protein_xref_uniprotkb", "A0A096MJY4" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "228", "228", "Phosphoserine", "ECO_0000250", "S", "", "protein_xref_pubmed", "Q06413" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "239", "239", "N6-acetyllysine", "ECO_0000250", "K", "", "protein_xref_uniprotkb", "A0A096MJY4" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "239", "239", "N6-acetyllysine", "ECO_0000250", "K", "", "protein_xref_pubmed", "Q06413" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "234", "234", "N6-acetyllysine", "ECO_0000250", "K", "", "protein_xref_uniprotkb", "A0A096MJY4" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "234", "234", "N6-acetyllysine", "ECO_0000250", "K", "", "protein_xref_pubmed", "Q06413" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "300", "300", "Phosphothreonine; by MAPK14", "ECO_0000250", "T", "", "protein_xref_uniprotkb", "A0A096MJY4" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "300", "300", "Phosphothreonine; by MAPK14", "ECO_0000250", "T", "", "protein_xref_pubmed", "Q06413" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "59", "59", "Phosphoserine; by CK2", "ECO_0000250", "S", "", "protein_xref_uniprotkb", "A0A096MJY4" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "59", "59", "Phosphoserine; by CK2", "ECO_0000250", "S", "", "protein_xref_pubmed", "Q8CFN5" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "293", "293", "Phosphothreonine; by MAPK14", "ECO_0000250", "T", "", "protein_xref_uniprotkb", "A0A096MJY4" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "293", "293", "Phosphothreonine; by MAPK14", "ECO_0000250", "T", "", "protein_xref_pubmed", "Q06413" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "264", "264", "N6-acetyllysine", "ECO_0000250", "K", "", "protein_xref_uniprotkb", "A0A096MJY4" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "264", "264", "N6-acetyllysine", "ECO_0000250", "K", "", "protein_xref_pubmed", "Q06413" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "119", "119", "N6-acetyllysine", "ECO_0000250", "K", "", "protein_xref_uniprotkb", "A0A096MJY4" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "119", "119", "N6-acetyllysine", "ECO_0000250", "K", "", "protein_xref_pubmed", "Q06413" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "445", "445", "Phosphoserine", "ECO_0000250", "S", "", "protein_xref_uniprotkb", "A0A096MJY4" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "445", "445", "Phosphoserine", "ECO_0000250", "S", "", "protein_xref_pubmed", "Q06413" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "4", "4", "N6-acetyllysine", "ECO_0000250", "K", "", "protein_xref_uniprotkb", "A0A096MJY4" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "4", "4", "N6-acetyllysine", "ECO_0000250", "K", "", "protein_xref_pubmed", "Q8CFN5" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "252", "252", "N6-acetyllysine", "ECO_0000250", "K", "", "protein_xref_uniprotkb", "A0A096MJY4" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "252", "252", "N6-acetyllysine", "ECO_0000250", "K", "", "protein_xref_pubmed", "Q06413" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "98", "98", "Phosphoserine", "ECO_0007744", "S", "", "protein_xref_uniprotkb", "A0A096MJY4" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "98", "98", "Phosphoserine", "ECO_0007744", "S", "", "protein_xref_pubmed", "22673903" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "240", "240", "Phosphoserine", "ECO_0007744", "S", "", "protein_xref_uniprotkb", "A0A096MJY4" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "240", "240", "Phosphoserine", "ECO_0007744", "S", "", "protein_xref_pubmed", "22673903" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "222", "222", "Phosphoserine", "ECO_0007744", "S", "", "protein_xref_uniprotkb", "A0A096MJY4" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "222", "222", "Phosphoserine", "ECO_0007744", "S", "", "protein_xref_pubmed", "22673903" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "110", "110", "Phosphoserine", "ECO_0007744", "S", "", "protein_xref_uniprotkb", "A0A096MJY4" ], [ "A0A096MJY4-1", "Mef2c", "Modified_Residue_Annotation", "110", "110", "Phosphoserine", "ECO_0007744", "S", "", "protein_xref_pubmed", "22673903" ], [ "A0A096MJY4-1", "Mef2c", "Nucleotide_Binding_Annotation", "58", "86", "Mef2-type", "", "ASTDMDKVLLKYTEYNEPHESRTNSDIVE", "", "protein_xref_uniprotkb", "A0A096MJY4" ], [ "P01946-1", "Hba1", "Metal_Binding_Annotation", "88", "88", "Iron (heme proximal ligand)", "", "H", "", "protein_xref_uniprotkb", "P01946" ], [ "P01946-1", "Hba1", "Metal_Binding_Annotation", "59", "59", "Iron (heme distal ligand)", "", "H", "", "protein_xref_uniprotkb", "P01946" ], [ "P01946-1", "Hba1", "Modified_Residue_Annotation", "125", "125", "Phosphoserine", "ECO_0000250", "S", "", "protein_xref_uniprotkb", "P01946" ], [ "P01946-1", "Hba1", "Modified_Residue_Annotation", "125", "125", "Phosphoserine", "ECO_0000250", "S", "", "protein_xref_pubmed", "P01942" ], [ "P01946-1", "Hba1", "Modified_Residue_Annotation", "103", "103", "Phosphoserine", "ECO_0000250", "S", "", "protein_xref_uniprotkb", "P01946" ], [ "P01946-1", "Hba1", "Modified_Residue_Annotation", "103", "103", "Phosphoserine", "ECO_0000250", "S", "", "protein_xref_pubmed", "P01942" ], [ "P01946-1", "Hba1", "Modified_Residue_Annotation", "8", "8", "N6-succinyllysine", "ECO_0000250", "K", "", "protein_xref_uniprotkb", "P01946" ] ] }, "readme": "Name\n - Rat Protein Site Annotation\n\nVersion\n - 1.11.2\n\nCreated on\n - 2019-12-04T12:24:09.578947\n\nModified on\n - 2022-01-12T16:37:01.593912\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 Protein Site Annotation (UniProtKB) dataset contains rat [taxid:10116] 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 sequences and extracts as a dataset in a csv format\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_masterlist.csv\n URI: https://data.glygen.org//ln2data/releases/data/v-1.11.2/reviewed/rat_protein_masterlist.csv\n Name: uniprot-proteome-rattus-norvegicus.nt\n URI: https://data.glygen.org//ln2data/releases/data/v-1.11.2/reviewed/rat_protein_ntdata.nt\n Output Subdomain\n Name: rat_protein_site_annotation_uniprotkb.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.12.1/reviewed/rat_protein_site_annotation_uniprotkb.csv\n Name: rat_protein_site_annotation_uniprotkb.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.12.1/reviewed/rat_protein_site_annotation_uniprotkb.stat.csv", "downloadurl": "/ln2data/releases/data/v-1.12.1/reviewed/rat_protein_site_annotation_uniprotkb.csv" }