{ "bcoid": "GLY_000317", "title": "Mouse Protein PTM Annotation (UniProtKB)", "description": "The Mouse Protein PTM Annotation (UniProtKB) dataset contains mouse [taxid:10090] PTM annotations for ...", "filename": "mouse_protein_ptm_annotation_uniprotkb.csv", "filetype": "csv", "categories": { "species": "Mus musculus", "molecule": "Protein", "tags": "PTM annotation", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "Q3URK3-1...", "protein_xref..." ], [ "Q3URK3-1...", "protein_xref..." ] ], "headers": [ "uniprotkb_ca...", "xref_key..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "eco_id" }, { "type": "string", "label": "ptm_annotation" } ], [ "Q3URK3-1", "protein_xref_uniprotkb", "Q3URK3", "ECO_0000269", "Glycosylated. Interaction with OGT leads to GlcNAcylation." ], [ "Q3URK3-1", "protein_xref_pubmed", "23352454", "ECO_0000269", "Glycosylated. Interaction with OGT leads to GlcNAcylation." ], [ "Q9EP73-1", "protein_xref_uniprotkb", "Q9EP73", "ECO_0000250", "Ubiquitinated; STUB1 likely mediates polyubiquitination of PD-L1/CD274 triggering its degradation." ], [ "Q9EP73-1", "protein_xref_pubmed", "Q9NZQ7", "ECO_0000250", "Ubiquitinated; STUB1 likely mediates polyubiquitination of PD-L1/CD274 triggering its degradation." ], [ "O08911-1", "protein_xref_uniprotkb", "O08911", "ECO_0000269", "Dually phosphorylated on Thr-183 and Tyr-185 by MAP2K3/MKK3 and MAP2K6/MKK6, which activates the enzyme." ], [ "O08911-1", "protein_xref_pubmed", "20004242", "ECO_0000269", "Dually phosphorylated on Thr-183 and Tyr-185 by MAP2K3/MKK3 and MAP2K6/MKK6, which activates the enzyme." ], [ "G5E8Q8-1", "protein_xref_uniprotkb", "G5E8Q8", "ECO_0000250", "Proteolytically cleaved at multiple sites: one in the GPS domain (S1 site) and the other in the SEA domain (S2 site). The proteolytic cleavage at S1 site generates an extracellular subunit and a seven-transmembrane subunit. The proteolytic cleavage at S2 site generates a fragment that undergoes proteolytic cleavage by the processing enzyme furin." ], [ "G5E8Q8-1", "protein_xref_pubmed", "Q9WVT0", "ECO_0000250", "Proteolytically cleaved at multiple sites: one in the GPS domain (S1 site) and the other in the SEA domain (S2 site). The proteolytic cleavage at S1 site generates an extracellular subunit and a seven-transmembrane subunit. The proteolytic cleavage at S2 site generates a fragment that undergoes proteolytic cleavage by the processing enzyme furin." ], [ "G5E8Q8-1", "protein_xref_uniprotkb", "G5E8Q8", "ECO_0000250", "Highly glycosylated." ], [ "G5E8Q8-1", "protein_xref_pubmed", "Q9WVT0", "ECO_0000250", "Highly glycosylated." ], [ "P50427-1", "protein_xref_uniprotkb", "P50427", "ECO_0000250", "The conversion to 3-oxoalanine (also known as C-formylglycine, FGly), of a serine or cysteine residue in prokaryotes and of a cysteine residue in eukaryotes, is critical for catalytic activity." ], [ "P50427-1", "protein_xref_pubmed", "P08842", "ECO_0000250", "The conversion to 3-oxoalanine (also known as C-formylglycine, FGly), of a serine or cysteine residue in prokaryotes and of a cysteine residue in eukaryotes, is critical for catalytic activity." ], [ "Q8VC03-1", "protein_xref_uniprotkb", "Q8VC03", "ECO_0000250", "Phosphorylation at Thr-882 during mitosis is required for interaction with TUBG1, HAUS1, HAUS2, HAUS3, HAUS4, HAUS5, HAUS6, HAUS7 and HAUS8 and their recruitement to spindle microtubules." ], [ "Q8VC03-1", "protein_xref_pubmed", "Q32P44", "ECO_0000250", "Phosphorylation at Thr-882 during mitosis is required for interaction with TUBG1, HAUS1, HAUS2, HAUS3, HAUS4, HAUS5, HAUS6, HAUS7 and HAUS8 and their recruitement to spindle microtubules." ], [ "P22727-1", "protein_xref_uniprotkb", "P22727", "ECO_0000250", "Palmitoleoylation is required for efficient binding to frizzled receptors. Depalmitoleoylation leads to Wnt signaling pathway inhibition." ], [ "P22727-1", "protein_xref_pubmed", "P27467", "ECO_0000250", "Palmitoleoylation is required for efficient binding to frizzled receptors. Depalmitoleoylation leads to Wnt signaling pathway inhibition." ], [ "P22727-1", "protein_xref_pubmed", "P56704", "ECO_0000250", "Palmitoleoylation is required for efficient binding to frizzled receptors. Depalmitoleoylation leads to Wnt signaling pathway inhibition." ], [ "Q8BGW0-1", "protein_xref_uniprotkb", "Q8BGW0", "ECO_0000269", "Phosphorylated on Tyr residues quickly after TCR stimulation." ], [ "Q8BGW0-1", "protein_xref_pubmed", "19597498", "ECO_0000269", "Phosphorylated on Tyr residues quickly after TCR stimulation." ], [ "Q8BGW0-1", "protein_xref_pubmed", "19597499", "ECO_0000269", "Phosphorylated on Tyr residues quickly after TCR stimulation." ], [ "Q9QZD9-1", "protein_xref_uniprotkb", "Q9QZD9", "ECO_0000255", "Phosphorylated by TGF-beta type II receptor." ], [ "Q9QZD9-1", "protein_xref_pubmed", "MF_03008", "ECO_0000255", "Phosphorylated by TGF-beta type II receptor." ], [ "Q91YI1-1", "protein_xref_uniprotkb", "Q91YI1", "ECO_0000250", "Phosphorylated by ULK1, ULK2 and mTOR. Phosphorylation status depends on nutrient-rich conditions; dephosphorylated during starvation or following treatment with rapamycin. ULK1-mediated phosphorylation of ATG13 at Ser-354 is required for efficient clearance of depolarized mitochondria." ], [ "Q91YI1-1", "protein_xref_pubmed", "O75143", "ECO_0000250", "Phosphorylated by ULK1, ULK2 and mTOR. Phosphorylation status depends on nutrient-rich conditions; dephosphorylated during starvation or following treatment with rapamycin. ULK1-mediated phosphorylation of ATG13 at Ser-354 is required for efficient clearance of depolarized mitochondria." ], [ "Q9WUZ9-1", "protein_xref_uniprotkb", "Q9WUZ9", "ECO_0000269", "N-glycosylated; high-mannose type." ], [ "Q9WUZ9-1", "protein_xref_pubmed", "21074248", "ECO_0000269", "N-glycosylated; high-mannose type." ], [ "Q9WUZ9-1", "protein_xref_pubmed", "10369669", "ECO_0000269", "N-glycosylated; high-mannose type." ], [ "Q69Z98-1", "protein_xref_uniprotkb", "Q69Z98", "ECO_0000269", "May be phosphorylated at Thr-261 by PKA (By similarity). Phosphorylated at Thr-175 by STK11/LKB1 in complex with STE20-related adapter-alpha (STRADA) pseudo kinase and CAB39. Not phosphorylated at Thr-175 by CaMKK2. In contrast, it is phosphorylated and activated by CaMKK1. May be inactivated via dephosphorylation of Thr-175 by PP2C." ], [ "Q69Z98-1", "protein_xref_pubmed", "17482548", "ECO_0000269", "May be phosphorylated at Thr-261 by PKA (By similarity). Phosphorylated at Thr-175 by STK11/LKB1 in complex with STE20-related adapter-alpha (STRADA) pseudo kinase and CAB39. Not phosphorylated at Thr-175 by CaMKK2. In contrast, it is phosphorylated and activated by CaMKK1. May be inactivated via dephosphorylation of Thr-175 by PP2C." ], [ "Q9ESN9-1", "protein_xref_uniprotkb", "Q9ESN9", "ECO_0000250", "Phosphorylation by ROCK1 is crucial for the recruitment of JNK." ], [ "Q9ESN9-1", "protein_xref_pubmed", "Q9UPT6", "ECO_0000250", "Phosphorylation by ROCK1 is crucial for the recruitment of JNK." ], [ "Q9ESN6-1", "protein_xref_uniprotkb", "Q9ESN6", "ECO_0000269", "RING-type zinc finger-dependent and UBE2D1-dependent autoubiquitination." ], [ "Q9ESN6-1", "protein_xref_pubmed", "18687884", "ECO_0000269", "RING-type zinc finger-dependent and UBE2D1-dependent autoubiquitination." ], [ "Q9ESN2-1", "protein_xref_uniprotkb", "Q9ESN2", "ECO_0000250", "Autoubiquitinated." ], [ "Q9ESN2-1", "protein_xref_pubmed", "Q9HCM9", "ECO_0000250", "Autoubiquitinated." ], [ "Q9ESN3-1", "protein_xref_uniprotkb", "Q9ESN3", "ECO_0000250", "Glycosylated." ], [ "Q9ESN3-1", "protein_xref_pubmed", "Q9HCN3", "ECO_0000250", "Glycosylated." ], [ "Q9D5T7-1", "protein_xref_uniprotkb", "Q9D5T7", "ECO_0000269", "Phosphorylated at Ser-375 in a SPO11-dependent manner." ], [ "Q9D5T7-1", "protein_xref_pubmed", "22346761", "ECO_0000269", "Phosphorylated at Ser-375 in a SPO11-dependent manner." ], [ "Q9D5T7-1", "protein_xref_pubmed", "19686734", "ECO_0000269", "Phosphorylated at Ser-375 in a SPO11-dependent manner." ], [ "O88307-1", "protein_xref_uniprotkb", "O88307", "ECO_0000250", "Within the Golgi apparatus, the propeptide may be cleaved off by FURIN or a furin-like protease. After cleavage, the propeptide interacts with the mature protein N-terminus, preventing the association with other ligands. At the cell surface, partially subjected to proteolytic shedding that releases the ectodomain in the extracellular milieu. The shedding may be catalyzed by ADAM17/TACE. Following shedding, PSEN1/presenilin-1 cleaves the remaining transmembrane fragment and catalyzes the release of a C-terminal fragment in the cytosol and of a soluble N-terminal beta fragment in the extracellular milieu. The C-terminal cytosolic fragment localizes to the nucleus." ], [ "O88307-1", "protein_xref_pubmed", "Q92673", "ECO_0000250", "Within the Golgi apparatus, the propeptide may be cleaved off by FURIN or a furin-like protease. After cleavage, the propeptide interacts with the mature protein N-terminus, preventing the association with other ligands. At the cell surface, partially subjected to proteolytic shedding that releases the ectodomain in the extracellular milieu. The shedding may be catalyzed by ADAM17/TACE. Following shedding, PSEN1/presenilin-1 cleaves the remaining transmembrane fragment and catalyzes the release of a C-terminal fragment in the cytosol and of a soluble N-terminal beta fragment in the extracellular milieu. The C-terminal cytosolic fragment localizes to the nucleus." ], [ "O88307-1", "protein_xref_uniprotkb", "O88307", "ECO_0000250", "Phosphorylation at Ser-2207 facilitates the interaction with GGA1." ], [ "O88307-1", "protein_xref_pubmed", "Q92673", "ECO_0000250", "Phosphorylation at Ser-2207 facilitates the interaction with GGA1." ], [ "P27467-1", "protein_xref_uniprotkb", "P27467", "ECO_0000269", "Disulfide bonds have critical and distinct roles in secretion and activity. Loss of each conserved cysteine in WNT3A results in high molecular weight oxidized Wnt oligomers, which are formed through inter-Wnt disulfide bonding." ], [ "P27467-1", "protein_xref_pubmed", "22726442", "ECO_0000269", "Disulfide bonds have critical and distinct roles in secretion and activity. Loss of each conserved cysteine in WNT3A results in high molecular weight oxidized Wnt oligomers, which are formed through inter-Wnt disulfide bonding." ], [ "P27467-1", "protein_xref_uniprotkb", "P27467", "ECO_0000269", "Proteolytic processing by TIKI1 and TIKI2 promotes oxidation and formation of large disulfide-bond oligomers, leading to inactivation of WNT3A." ], [ "P27467-1", "protein_xref_pubmed", "22726442", "ECO_0000269", "Proteolytic processing by TIKI1 and TIKI2 promotes oxidation and formation of large disulfide-bond oligomers, leading to inactivation of WNT3A." ], [ "P27467-1", "protein_xref_uniprotkb", "P27467", "ECO_0000250", "Palmitoleoylation by PORCN is required for efficient binding to frizzled receptors. Palmitoleoylation is required for proper trafficking to cell surface, vacuolar acidification is critical to release palmitoleoylated WNT3A from WLS in secretory vesicles (PubMed:17141155, PubMed:24798332). Depalmitoleoylated by NOTUM, leading to inhibit Wnt signaling pathway, possibly by promoting disulfide bond formation and oligomerization (PubMed:25771893)." ], [ "P27467-1", "protein_xref_pubmed", "P56704", "ECO_0000250", "Palmitoleoylation by PORCN is required for efficient binding to frizzled receptors. Palmitoleoylation is required for proper trafficking to cell surface, vacuolar acidification is critical to release palmitoleoylated WNT3A from WLS in secretory vesicles (PubMed:17141155, PubMed:24798332). Depalmitoleoylated by NOTUM, leading to inhibit Wnt signaling pathway, possibly by promoting disulfide bond formation and oligomerization (PubMed:25771893)." ], [ "P27467-1", "protein_xref_uniprotkb", "P27467", "ECO_0000269", "Palmitoleoylation by PORCN is required for efficient binding to frizzled receptors. Palmitoleoylation is required for proper trafficking to cell surface, vacuolar acidification is critical to release palmitoleoylated WNT3A from WLS in secretory vesicles (PubMed:17141155, PubMed:24798332). Depalmitoleoylated by NOTUM, leading to inhibit Wnt signaling pathway, possibly by promoting disulfide bond formation and oligomerization (PubMed:25771893)." ], [ "P27467-1", "protein_xref_pubmed", "24798332", "ECO_0000269", "Palmitoleoylation by PORCN is required for efficient binding to frizzled receptors. Palmitoleoylation is required for proper trafficking to cell surface, vacuolar acidification is critical to release palmitoleoylated WNT3A from WLS in secretory vesicles (PubMed:17141155, PubMed:24798332). Depalmitoleoylated by NOTUM, leading to inhibit Wnt signaling pathway, possibly by promoting disulfide bond formation and oligomerization (PubMed:25771893)." ], [ "P27467-1", "protein_xref_pubmed", "25771893", "ECO_0000269", "Palmitoleoylation by PORCN is required for efficient binding to frizzled receptors. Palmitoleoylation is required for proper trafficking to cell surface, vacuolar acidification is critical to release palmitoleoylated WNT3A from WLS in secretory vesicles (PubMed:17141155, PubMed:24798332). Depalmitoleoylated by NOTUM, leading to inhibit Wnt signaling pathway, possibly by promoting disulfide bond formation and oligomerization (PubMed:25771893)." ], [ "P27467-1", "protein_xref_pubmed", "17141155", "ECO_0000269", "Palmitoleoylation by PORCN is required for efficient binding to frizzled receptors. Palmitoleoylation is required for proper trafficking to cell surface, vacuolar acidification is critical to release palmitoleoylated WNT3A from WLS in secretory vesicles (PubMed:17141155, PubMed:24798332). Depalmitoleoylated by NOTUM, leading to inhibit Wnt signaling pathway, possibly by promoting disulfide bond formation and oligomerization (PubMed:25771893)." ], [ "Q8VEK3-1", "protein_xref_uniprotkb", "Q8VEK3", "ECO_0000250", "Cleaved at Asp-94 by CASP3 during T-cell apoptosis, resulting in a loss of DNA- and chromatin-binding activities." ], [ "Q8VEK3-1", "protein_xref_pubmed", "Q00839", "ECO_0000250", "Cleaved at Asp-94 by CASP3 during T-cell apoptosis, resulting in a loss of DNA- and chromatin-binding activities." ], [ "Q8VEK3-1", "protein_xref_uniprotkb", "Q8VEK3", "ECO_0000250", "Extensively phosphorylated. Phosphorylated on Ser-58 by PLK1 and dephosphorylated by protein phosphatase 2A (PP2A) in mitosis." ], [ "Q8VEK3-1", "protein_xref_pubmed", "Q00839", "ECO_0000250", "Extensively phosphorylated. Phosphorylated on Ser-58 by PLK1 and dephosphorylated by protein phosphatase 2A (PP2A) in mitosis." ], [ "Q8VEK3-1", "protein_xref_uniprotkb", "Q8VEK3", "ECO_0000269", "Citrullinated by PADI4." ], [ "Q8VEK3-1", "protein_xref_pubmed", "24463520", "ECO_0000269", "Citrullinated by PADI4." ], [ "Q8VEK0-1", "protein_xref_uniprotkb", "Q8VEK0", "ECO_0000269", "N-glycosylated. Contains high mannose-type oligosaccharides." ], [ "Q8VEK0-1", "protein_xref_pubmed", "22253360", "ECO_0000269", "N-glycosylated. Contains high mannose-type oligosaccharides." ], [ "Q8C0V1-1", "protein_xref_uniprotkb", "Q8C0V1", "ECO_0000269", "Phosphorylated by CDK (PubMed:24413433, PubMed:26548954). Phosphorylation by CDK takes place in late prophase when the cap exchange is prominent (PubMed:26548954). is important for the stabilization of telomere attachment but dispenable for the cap exchange (PubMed:26548954)." ], [ "Q8C0V1-1", "protein_xref_pubmed", "26548954", "ECO_0000269", "Phosphorylated by CDK (PubMed:24413433, PubMed:26548954). Phosphorylation by CDK takes place in late prophase when the cap exchange is prominent (PubMed:26548954). is important for the stabilization of telomere attachment but dispenable for the cap exchange (PubMed:26548954)." ], [ "Q8C0V1-1", "protein_xref_pubmed", "24413433", "ECO_0000269", "Phosphorylated by CDK (PubMed:24413433, PubMed:26548954). Phosphorylation by CDK takes place in late prophase when the cap exchange is prominent (PubMed:26548954). is important for the stabilization of telomere attachment but dispenable for the cap exchange (PubMed:26548954)." ], [ "Q9R001-1", "protein_xref_uniprotkb", "Q9R001", "ECO_0000250", "The precursor is cleaved by furin and PCSK7 outside of the cell." ], [ "Q9R001-1", "protein_xref_pubmed", "Q9UNA0", "ECO_0000250", "The precursor is cleaved by furin and PCSK7 outside of the cell." ], [ "Q9R007-3", "protein_xref_uniprotkb", "Q9R007", "ECO_0000269", "N-glycosylated (PubMed:19074552, PubMed:19251634). Contains sialic acid residues (PubMed:19074552)." ], [ "Q9R007-3", "protein_xref_pubmed", "19074552", "ECO_0000269", "N-glycosylated (PubMed:19074552, PubMed:19251634). Contains sialic acid residues (PubMed:19074552)." ], [ "Q9R007-3", "protein_xref_pubmed", "19251634", "ECO_0000269", "N-glycosylated (PubMed:19074552, PubMed:19251634). Contains sialic acid residues (PubMed:19074552)." ], [ "Q6QIY3-1", "protein_xref_uniprotkb", "Q6QIY3", "ECO_0000250", "Lacks the cysteine which covalently binds the conotoxin GVIIJ. This cysteine (position 815) is speculated in other sodium channel subunits alpha to be implied in covalent binding with the sodium channel subunit beta-2 or beta-4." ], [ "Q6QIY3-1", "protein_xref_pubmed", "P15389", "ECO_0000250", "Lacks the cysteine which covalently binds the conotoxin GVIIJ. This cysteine (position 815) is speculated in other sodium channel subunits alpha to be implied in covalent binding with the sodium channel subunit beta-2 or beta-4." ], [ "O70131-1", "protein_xref_uniprotkb", "O70131", "ECO_0000269", "Cleaved by MMP9 protease to generate the Secreted ninjurin-1 form." ], [ "O70131-1", "protein_xref_pubmed", "23142597", "ECO_0000269", "Cleaved by MMP9 protease to generate the Secreted ninjurin-1 form." ], [ "O70131-1", "protein_xref_pubmed", "32883094", "ECO_0000269", "Cleaved by MMP9 protease to generate the Secreted ninjurin-1 form." ], [ "O70131-1", "protein_xref_uniprotkb", "O70131", "ECO_0000269", "N-linked glycosylation is required for homooligomerization." ], [ "O70131-1", "protein_xref_pubmed", "28067406", "ECO_0000269", "N-linked glycosylation is required for homooligomerization." ], [ "O70133-1", "protein_xref_uniprotkb", "O70133", "ECO_0000250", "Phosphorylated by PRKDC; phosphorylation occurs in a RNA-dependent manner. Phosphorylated by EIF2AK2/PKR; this phosphorylation reduces its association with double-stranded RNA." ], [ "O70133-1", "protein_xref_pubmed", "Q08211", "ECO_0000250", "Phosphorylated by PRKDC; phosphorylation occurs in a RNA-dependent manner. Phosphorylated by EIF2AK2/PKR; this phosphorylation reduces its association with double-stranded RNA." ], [ "O70133-1", "protein_xref_uniprotkb", "O70133", "ECO_0000250", "Methylated. PRMT1-mediated methylation of undefined Arg residues in the nuclear transport domain (NTD) is required for nuclear import of DHX9." ], [ "O70133-1", "protein_xref_pubmed", "Q08211", "ECO_0000250", "Methylated. PRMT1-mediated methylation of undefined Arg residues in the nuclear transport domain (NTD) is required for nuclear import of DHX9." ], [ "Q5S248-1", "protein_xref_uniprotkb", "Q5S248", "ECO_0000269", "N-glycosylated." ], [ "Q5S248-1", "protein_xref_pubmed", "15328353", "ECO_0000269", "N-glycosylated." ], [ "Q61618-1", "protein_xref_uniprotkb", "Q61618", "ECO_0000250", "Phosphorylation on Thr-317 and Thr-318 may be crucial for rapid desensitization. Phosphorylation on Thr-317 may be necessary for phosphorylation on Thr-318 to occur." ] ] }, "readme": "Name\n - Mouse Protein PTM Annotation (UniProtKB)\n\nVersion\n - 1.11.2\n\nCreated on\n - 2019-11-30T14:05:28.986536\n\nModified on\n - 2022-01-18T12:00:14.006361\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 Mouse Protein PTM Annotation (UniProtKB) dataset contains mouse [taxid:10090] PTM annotations for UniProtKB canonical accessions. The annotation is the curated statements of mainly about glycosylation and phosphorylation. 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 - ptm annotation\n - glycosylation\n - phosphorylation\n\n Pipeline Steps\n - Step-1: The script extracts the ptm annotation strings 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: uniprot-proteome-mus-musculus.nt\n URI: https://data.glygen.org/ln2data/releases/data/v-1.11.2/reviewed/uniprot-proteome-mus-musculus.nt\n Name: mouse_protein_masterlist.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.11.2/reviewed/mouse_protein_masterlist.csv\n Output Subdomain\n Name: mouse_protein_ptm_annotation_uniprotkb.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.11.2/reviewed/mouse_protein_ptm_annotation_uniprotkb.csv\n Name: mouse_protein_ptm_annotation_uniprotkb.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.11.2/reviewed/mouse_protein_ptm_annotation_uniprotkb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"16\"\n Name: \"motif_start\"\n Description: \"\"\n Unique Values: \"23\"\n Name: \"filter_flags\"\n Description: \"Filter tags/flags assigned to the mutation entries that have passed the mutation filter criteria\"\n Unique Values: \"19\"\n Name: \"sift_prediction\"\n Description: \"The SIFT qualitative prediction is derived from this score such that substitutions with a score < 0.05 are called 'deleterious' and all others are called 'tolerated\"\n Unique Values: \"3\"\n Name: \"somatic_status\"\n Description: \"The status of the variant whether it is germline (somatic status =0) or somatic (somatic status =1) variant\"\n Unique Values: \"1\"\n Name: \"chr_pos\"\n Description: \"Chromosome Position of a gene\"\n Unique Values: \"19\"\n Name: \"chr_id\"\n Description: \"\"\n Unique Values: \"10\"\n Name: \"dbsnp_id\"\n Description: \"\"A reference SNP ID number\"\n Unique Values: \"19\"\n Name: \"evidence_ECO:0000313\"\n Description: \"A type of evidence that is imported information used in an automatic assertion\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"19\"\n Name: \"mim_id\"\n Description: \"Disease ID from the OMIM database\"\n Unique Values: \"1\"\n Name: \"description\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"begin_aa_pos\"\n Description: \"Start position of the amino acid in the sequence of a protein in UniProtKB\"\n Unique Values: \"18\"\n Name: \"cytogenic_band\"\n Description: \"One of the subregions of a chromosome visible microscopically after special staining\"\n Unique Values: \"14\"\n Name: \"aa_pos\"\n Description: \"Position of the amino acid in canonical sequence of protein in the UniProtKB database\"\n Unique Values: \"18\"\n Name: \"ref_aa\"\n Description: \"Reference amino acid residue\"\n Unique Values: \"9\"\n Name: \"sift_score\"\n Description: \"SIFT predicts whether an amino acid substitution is likely to affect protein function based on sequence homology and the physico-chemical similarity between the alternate amino acids. The data we provide for each amino acid substitution is a score and a qualitative prediction (either 'tolerated' or 'deleterious'). The score is the normalized probability that the amino acid change is tolerated so scores nearer zero are more likely to be deleterious. The qualitative prediction is derived from this score such that substitutions with a score < 0.05 are called 'deleterious' and all others are called 'tolerated\"\n Unique Values: \"10\"\n Name: \"alt_motif\"\n Description: \"Altered motif\"\n Unique Values: \"24\"\n Name: \"disease_xrefs\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"polyphen_score\"\n Description: \"The score assigned to a amino acid substitution by a tool called as PolyPhen (=Polymorphism Phenotyping) which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations. The PolyPhen score ranges from 0.0 (tolerated) to 1.0 (deleterious). Variants with scores of 0.0 are predicted to be benign. Values closer to 1.0 are more confidently predicted to be deleterious\"\n Unique Values: \"1\"\n Name: \"polyphen_prediction\"\n Description: \"\"The PolyPhen prediction values are - greater than 0.908 - \"\"Probably Damaging\"\"; greater than 0.446 and less than or equal to 0.908 - \"\"Possibly Damaging\"\"; less than or equal to 0.446 - \"\"Benign\"\"\"\n Unique Values: \"1\"\n Name: \"is_known_glycoprotein\"\n Description: \"Yes or no flag to denote if a protein is experimentally proven glycoprotein\"\n Unique Values: \"1\"\n Name: \"alt_nt\"\n Description: \"Alternative nucleotide\"\n Unique Values: \"1\"\n Name: \"protein_name\"\n Description: \"Protein name in the UniProtKB\"\n Unique Values: \"16\"\n Name: \"disease_evidence_ECO:0000313\"\n Description: \"The evidence that could be a PMID or a ClinVar ID that associates disease with the variant\"\n Unique Values: \"1\"\n Name: \"effect\"\n Description: \"The effect on glycosylation or N-sequon due to variation at site of glycosylated amino acid.\"\n Unique Values: \"3\"\n Name: \"end_aa_pos\"\n Description: \"End position of the amino acid in the sequence of a protein in UniProtKB\"\n Unique Values: \"18\"\n Name: \"mutation_type\"\n Description: \"Denotes whether mutation was reported with reference to amino acid or nucleotide\"\n Unique Values: \"1\"\n Name: \"disease_description\"\n Description: \"The disease description and/or definition \"\n Unique Values: \"1\"\n Name: \"do_id\"\n Description: \"Disease Ontology identifier\"\n Unique Values: \"1\"\n Name: \"evidence_ECO:0000269\"\n Description: \"A type of experimental evidence that is used in a manual assertion. Usually the values are PMIDs\"\n Unique Values: \"1\"\n Name: \"ref_nt\"\n Description: \"Reference nucleotide\"\n Unique Values: \"4\"\n Name: \"disease\"\n Description: \"The disease name for the cell line\"\n Unique Values: \"1\"\n Name: \"alt_aa\"\n Description: \"Altered amino acid residue\"\n Unique Values: \"10\"\n Name: \"cosmic_id\"\n Description: \"Legacy mutation identifier (COSM) in Catalogue of Somatic Mutations in Cancer (COSMIC) represents existing COSM mutation identifiers. This identifier remains the same between different assemblies (GRCh37 and GRCh38). All the COSM ids at the same genomic location have been collapsed into one representative COSM id. These ids are maintained to help track existing mutations\"\n Unique Values: \"1\"\n Name: \"ref_motif\"\n Description: \"Reference motif\"\n Unique Values: \"20\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"2\"\n Name: \"minor_allelic_frequency\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"gene_name\"\n Description: \"\"Official gene name/symbol assigned to the gene. Human gene name/symbol are approved by the HUGO Gene Nomenclature Committee (HGNC) and mouse gene name are approved by the Mouse Genome Informatics (MGI)\"\n Unique Values: \"17\"\n Name: \"disease_evidence_ECO:0000269\"\n Description: \"The PMID evidence for the association of the disease with the variant.\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.11.2/reviewed/mouse_protein_ptm_annotation_uniprotkb.csv" }