{ "bcoid": "GLY_000275", "title": "Rat Protein Information (NCBI RefSeq)", "description": "The Rat Protein Information (NCBI RefSeq) dataset contains rat [taxid:10116] protein information such ...", "filename": "rat_protein_info_refseq.csv", "filetype": "csv", "categories": { "species": [ "Rattus norvegicus" ], "molecule": [ "Protein" ], "tag": [ "Protein Information" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "Robel...", " mapped NP_0..." ], [ "Robel...", " feat NP_001..." ] ], "headers": [ "uniprotkb_ca...", "p_refseq_ac_..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "p_refseq_ac_best_match" }, { "type": "string", "label": "refseq_protein_name" }, { "type": "string", "label": "refseq_protein_length" }, { "type": "string", "label": "refseq_protein_summary" } ], [ "Robel", " mapped NP_001102640" ], [ "Robel", " feat NP_001102640" ], [ "M0R5G2-1", "NP_001102640", "gem-associated protein 7", "143", "" ], [ "Robel", " mapped NP_001000696" ], [ "Robel", " feat NP_001000696" ], [ "D3ZQX7-1", "NP_001000696", "olfactory receptor Olr1845", "317", "Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008]. " ], [ "Robel", " mapped NP_001101129" ], [ "Robel", " feat NP_001101129" ], [ "D3ZTD8-1", "NP_001101129", "semaphorin-5A precursor", "1074", "" ], [ "Robel", " mapped NP_037015" ], [ "Robel", " feat NP_037015" ], [ "P52844-1", "NP_037015", "estrogen sulfotransferase", "295", "isozyme that catalyzes the sulfation of estrogens, including beta-estradiol and estrone, but not of dehydroepiandrosterone, pregnenolone, cortisol or testosterone; plays a role in estrogen metabolism [RGD, Feb 2006]. " ], [ "Robel", " mapped NP_001129388" ], [ "Robel", " feat NP_001129388" ], [ "B2ZEZ3-1", "NP_001129388", "selection and upkeep of intraepithelial T-cells protein 1 precursor", "377", "" ], [ "Robel", " mapped NP_001157911" ], [ "Robel", " feat NP_001157911" ], [ "D3ZW63-1", "NP_001157911", "transmembrane protein 212 isoform 2", "187", "" ], [ "Robel", " mapped NP_001101660" ], [ "Robel", " feat NP_001101660" ], [ "D4A1N0-1", "NP_001101660", "receptor-transporting protein 3", "465", "" ], [ "Robel", " mapped NP_001276666" ], [ "Robel", " feat NP_001276666" ], [ "P24623-1", "NP_001276666", "alpha-crystallin A chain isoform 2", "196", "This gene encodes subunit a, one of two subunits of alpha-crystallin, which is a high molecular weight, soluble aggregate and is a member of the small heat shock protein family. The encoded protein has been identified as a moonlighting protein based on its ability to perform mechanistically distinct functions. It acts as a molecular chaperone and is the major protein in the eye lens, maintaining the transparency and refractive index of the lens. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]. " ], [ "Robel", " mapped NP_001303262" ], [ "Robel", " feat NP_001303262" ], [ "P42123-1", "NP_001303262", "L-lactate dehydrogenase B chain isoform Ldhbx", "341", "This gene encodes the B subunit of lactate dehydrogenase enzyme, which catalyzes the interconversion of pyruvate and lactate with concomitant interconversion of NADH and NAD+ in a post-glycolysis process. Alternatively spliced transcript variants have also been found for this gene. Recent studies have shown that a C-terminally extended isoform is produced by use of an alternative in-frame translation termination codon via a stop codon readthrough mechanism, and that this isoform is localized in the peroxisomes. Pseudogenes have been identified on chromosomes X and 9. [provided by RefSeq, Feb 2016]. " ], [ "Robel", " mapped NP_001029179" ], [ "Robel", " feat NP_001029179" ], [ "B1H215-1", "NP_001029179", "nuclear receptor coactivator 4", "622", "" ], [ "Robel", " mapped NP_001040563" ], [ "Robel", " feat NP_001040563" ], [ "A0A8I5ZU93-1", "NP_001040563", "COP9 signalosome complex subunit 7a isoform 2", "277", "" ], [ "Robel", " mapped NP_001185509" ], [ "Robel", " feat NP_001185509" ], [ "M0R9L0-1", "NP_001185509", "nascent polypeptide-associated complex subunit alpha isoform 2", "2163", "" ], [ "Robel", " mapped NP_001100216" ], [ "Robel", " feat NP_001100216" ], [ "D4A6X4-1", "NP_001100216", "acylphosphatase-1", "99", "" ], [ "Robel", " mapped NP_001258103" ], [ "Robel", " feat NP_001258103" ], [ "A0A8I6AS21-1", "NP_001258103", "serine/threonine-protein phosphatase 4 regulatory subunit 3A isoform 1", "833", "" ], [ "Robel", " mapped NP_001101634" ], [ "Robel", " feat NP_001101634" ], [ "D4A3V5-1", "NP_001101634", "cingulin-like protein 1", "1292", "" ], [ "Robel", " mapped NP_001300931" ], [ "Robel", " feat NP_001300931" ], [ "D3ZJ87-1", "NP_001300931", "nephrocystin-1 isoform a", "701", "" ], [ "Robel", " mapped NP_001093991" ], [ "Robel", " feat NP_001093991" ], [ "F1LME7-1", "NP_001093991", "pleckstrin homology-like domain family A member 2 isoform 1", "138", "" ], [ "Robel", " mapped NP_001099351" ], [ "Robel", " feat NP_001099351" ], [ "D4A5Y6-1", "NP_001099351", "N-alpha-acetyltransferase 50 isoform 2", "168", "" ], [ "Robel", " mapped NP_665731" ], [ "Robel", " feat NP_665731" ], [ "A0A0G2K130-1", "NP_665731", "TRAF family member-associated NF-kappa-B activator isoform 1", "414", "" ], [ "Robel", " mapped NP_001019445" ], [ "Robel", " feat NP_001019445" ], [ "Q53E76-1", "NP_001019445", "glycosyltransferase-like domain-containing protein 1 isoform 2", "389", "" ], [ "Robel", " mapped NP_001102701" ], [ "Robel", " feat NP_001102701" ], [ "D3ZA60-1", "NP_001102701", "leucine-rich repeat-containing protein 61", "259", "" ], [ "Robel", " mapped NP_001012126" ], [ "Robel", " feat NP_001012126" ], [ "Q5M7A3-1", "NP_001012126", "solute carrier family 35 member G2", "412", "" ], [ "Robel", " mapped NP_001012046" ], [ "Robel", " feat NP_001012046" ], [ "Q5HZA2-1", "NP_001012046", "protein sprouty homolog 2", "314", "" ], [ "Robel", " mapped NP_001100089" ], [ "Robel", " feat NP_001100089" ], [ "D3ZVQ0-1", "NP_001100089", "ubiquitin carboxyl-terminal hydrolase 5 isoform 1", "858", "" ], [ "Robel", " mapped NP_001020806" ], [ "Robel", " feat NP_001020806" ], [ "F1LPV0-1", "NP_001020806", "asparagine--tRNA ligase, cytoplasmic isoform 1", "558", "" ], [ "Robel", " mapped NP_001102111" ], [ "Robel", " feat NP_001102111" ], [ "D4A6T2-1", "NP_001102111", "mitochondrial mRNA pseudouridine synthase RPUSD3 isoform 2", "320", "" ], [ "Robel", " mapped NP_001102149" ], [ "Robel", " feat NP_001102149" ], [ "B2RZB3-1", "NP_001102149", "protein eva-1 homolog B isoform 1", "225", "" ], [ "Robel", " mapped NP_001102525" ], [ "Robel", " feat NP_001102525" ], [ "D4ADI9-1", "NP_001102525", "WD repeat-containing protein 53", "358", "" ] ] }, "readme": "Name\n - Rat Protein Information (NCBI RefSeq)\n\nVersion\n - v-2.4.1\n\nCreated on\n - 2019-09-06T14:06:39.001496\n\nModified on\n - 2022-09-26T09:04:47.937314\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Luke Johnson [luke.johnson@email.gwu.edu], Urnisha Bhuiyan [sbhuiyan28@email.gwu.edu], Cyrus Au-Yeung [cyruschauyeung@gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu]\n\nAuthors\n - \n\nChecksum\n - \n\nUsability Domain\n - The Rat Protein Information (NCBI RefSeq) dataset contains rat [taxid:10116] protein information such as protein accession, name, length and protein function summary from NCBI RefSeq database. The dataset is derived from NCBI RefSeq Release 96, September 9, 2019. If you use this dataset please provide proper attribution to NCBI RefSeq and GlyGen\n\nDescription Domain\n Keywords\n - protein information\n - protein length\n - NCBI RefSeq\n - protein summary\n\n Pipeline Steps\n - Step-1: The script parses the NCBI RefSeq gpff files to extract the accession, length, protein summary and then maps the NCBI RefSeq accesion to the UniProtKB Canonical accessions\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_xref_refseq.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/rat_protein_xref_refseq.csv\n Name: refseq_protein_all_10116.gpff\n URI: https:/data.glygen.org/ln2downloads/ncbi/refseq/2024_02_18/refseq_protein_all_10116.gpff\n Output Subdomain\n Name: rat_protein_info_refseq.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/rat_protein_info_refseq.csv\n Name: rat_protein_info_refseq.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/rat_protein_info_refseq.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"12752\"\n Name: \"p_refseq_ac_best_match\"\n Description: \"Best match NCBI RefSeq protein accession to UniProtKB canonical accession\"\n Unique Values: \"38253\"\n Name: \"refseq_protein_name\"\n Description: \"Name of the protein in NCBI RefSeq database\"\n Unique Values: \"12733\"\n Name: \"refseq_protein_length\"\n Description: \"Length of the protein in NCBI RefSeq database\"\n Unique Values: \"1617\"\n Name: \"refseq_protein_summary\"\n Description: \"Function of the protein in NCBI RefSeq database\"\n Unique Values: \"138\"", "downloadurl": "/ln2data/releases/data/v-2.4.1/reviewed/rat_protein_info_refseq.csv" }