{ "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": [ [ "M0R5G2-1...", "NP_001102640..." ], [ "A0A8I6GFJ8-1...", "NP_001000790..." ] ], "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" } ], [ "M0R5G2-1", "NP_001102640", "gem-associated protein 7", "143", "" ], [ "A0A8I6GFJ8-1", "NP_001000790", "olfactory receptor Olr1331", "312", "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]. " ], [ "F1LT09-1", "NP_001100868", "pre-mRNA 3' end processing protein WDR33", "1331", "" ], [ "D3ZFQ5-1", "NP_001162101", "cadherin-9 precursor", "788", "" ], [ "D3ZRJ7-1", "NP_001178553", "leucine-rich repeat serine/threonine-protein kinase 1", "2013", "" ], [ "D4ADS6-1", "NP_001178604", "integrator complex subunit 7", "967", "" ], [ "P15393-1", "NP_036669", "cytochrome P450 11B1, mitochondrial precursor", "499", "catalyzes the conversion of 11-deoxycorticosterone to corticosterone [RGD, Feb 2006]. " ], [ "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]. " ], [ "D4A2F3-1", "NP_001000729", "olfactory receptor Olr1539", "306", "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]. " ], [ "D3ZZQ1-1", "NP_001099425", "abnormal spindle-like microcephaly-associated protein", "3133", "" ], [ "A0A8I5ZN56-1", "NP_001178874", "receptor-type tyrosine-protein phosphatase H precursor", "971", "may act as a protein tyrosine phosphatase [RGD, Feb 2006]. " ], [ "Q6ED65-1", "NP_001003402", "echinoderm microtubule-associated protein-like 5", "1977", "" ], [ "Q99MU5-1", "NP_599219", "spermatogenesis-associated protein 6 precursor", "488", "may function as a molecular motor in meiosis and have a role in spermatogenesis [RGD, Feb 2006]. " ], [ "D3ZTD8-1", "NP_001101129", "semaphorin-5A precursor", "1074", "" ], [ "D4ABL9-1", "NP_001296386", "coiled-coil domain-containing protein 151", "595", "" ], [ "Q8R4C0-1", "NP_604456", "calpain-5", "640", "human and mouse homologs are members of a subset of the calpain family of proteases that lack a calmodulin-like domain [RGD, Feb 2006]. " ], [ "P49889-1", "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]. " ], [ "B2ZEZ3-1", "NP_001129388", "selection and upkeep of intraepithelial T-cells protein 1 precursor", "377", "" ], [ "A0A8I6GH88-1", "NP_001127900", "peptidyl-prolyl cis-trans isomerase FKBP2 precursor", "140", "" ], [ "F1M1E4-1", "NP_001128225", "probable hydrolase PNKD isoform 3", "142", "" ], [ "A0A0G2KB91-1", "NP_001128560", "zinc finger protein 385A isoform 1", "415", "" ], [ "A0A0G2K2C7-1", "NP_001129365", "probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform 1", "2547", "" ], [ "D3ZGH9-1", "NP_001156403", "POM121-like protein 2 isoform 2", "519", "" ], [ "D3ZW63-1", "NP_001157911", "transmembrane protein 212 isoform 2", "187", "" ], [ "D4A1N0-1", "NP_001101660", "receptor-transporting protein 3", "465", "" ], [ "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]. " ], [ "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]. " ], [ "A0A8I5ZY32-1", "NP_001020288", "EH domain-binding protein 1-like protein 1 isoform 1", "774", "" ], [ "A0A0G2K6W6-1", "NP_001102477", "DIS3-like exonuclease 2 isoform 1", "890", "" ], [ "F1LYS7-1", "NP_001102499", "delta-sarcoglycan isoform a", "255", "" ], [ "F1LN87-1", "NP_001020932", "MAP kinase-activated protein kinase 5 isoform 2", "372", "" ], [ "A0A8I6A3B1-1", "NP_001029179", "nuclear receptor coactivator 4", "622", "" ], [ "A0A8I6G3E2-1", "NP_001103048", "uncharacterized protein LOC690326 precursor", "166", "" ], [ "A0A8I5ZU93-1", "NP_001040563", "COP9 signalosome complex subunit 7a isoform 2", "277", "" ], [ "D3ZF56-1", "NP_001072116", "transmembrane protein 134 isoform b", "180", "" ], [ "A0A0G2JUK7-1", "NP_001009498", "immunoreceptor Ly49si2", "267", "" ], [ "A0A8I6B415-1", "NP_001128328", "dual specificity protein phosphatase CDC14A isoform 1", "597", "The protein encoded by this gene is a dual-specificity phosphatase that preferentially dephosphorylates cyclin dependent kinase substrates to regulate the cell cycle. In human cell lines, this protein localizes to interphase chromosomes, and depletion of the transcript results in centrosome separation and cytokinesis defects. In mouse, the protein localizes to the nucleus of prophase I arrested oocytes and then becomes dispersed in meiotically competent oocytes. Knockdown of the protein delays exit from metaphase I and results in eggs with chromosomal abnormalities and elevated aneuploidy, demonstrating a function in regulation of meiosis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2015]. " ], [ "A0A0G2K492-1", "NP_001136417", "zinc finger protein 68 isoform 2", "554", "" ], [ "M0R9L0-1", "NP_001185509", "nascent polypeptide-associated complex subunit alpha isoform 2", "2163", "" ], [ "D4A4K6-1", "NP_001100913", "nebulin-related-anchoring protein isoform C", "1692", "" ], [ "D4A6X4-1", "NP_001100216", "acylphosphatase-1", "99", "" ], [ "A0A0G2K420-1", "NP_001264143", "POZ-, AT hook-, and zinc finger-containing protein 1 isoform 2", "537", "" ], [ "D3Z8G8-1", "NP_001264235", "MAU2 chromatid cohesion factor homolog isoform 2", "104", "" ], [ "D4A2I6-1", "NP_001292054", "transmembrane protein 220 isoform 2", "94", "" ], [ "D4A3E8-1", "NP_001102013", "28S ribosomal protein S27, mitochondrial isoform 2", "96", "" ], [ "Q5XIT5-1", "NP_001012181", "ETS-related transcription factor Elf-2 isoform 2", "519", "" ], [ "A0A8I6AS21-1", "NP_001258103", "serine/threonine-protein phosphatase 4 regulatory subunit 3A isoform 1", "833", "" ], [ "M0R4X8-1", "NP_001099376", "SUMO-specific isopeptidase USPL1 isoform 2", "518", "" ], [ "A0A0G2JVX9-1", "NP_001128518", "cAMP-regulated phosphoprotein 21 isoform 1", "88", "" ], [ "D4A3V5-1", "NP_001101634", "cingulin-like protein 1", "1292", "" ], [ "D3ZJ87-1", "NP_001300931", "nephrocystin-1 isoform a", "701", "" ], [ "D3ZQA1-1", "NP_001100621", "polypeptide N-acetylgalactosaminyltransferase 9 isoform B", "237", "" ], [ "A0A0G2KB91-1", "NP_001128561", "zinc finger protein 385A isoform 3", "366", "" ], [ "A0A0G2JYQ2-1", "NP_001258208", "homeobox protein PKNOX2 isoform 2", "446", "" ], [ "D3ZZ68-1", "NP_001292068", "synaptopodin 2-like protein isoform 2", "749", "" ], [ "F1MAS1-1", "NP_001101540", "voltage-dependent calcium channel beta subunit-associated regulatory protein", "431", "" ], [ "A0A8I6GKH8-1", "NP_001185567", "ensconsin isoform 2", "648", "" ], [ "D4A2T2-1", "NP_001101733", "Golgi apparatus membrane protein TVP23 homolog A isoform 1", "222", "" ], [ "A0A8I6GKX8-1", "NP_001264315", "IQ motif and SEC7 domain-containing protein 2 isoform 2", "949", "" ], [ "A0A8I5Y8F2-1", "NP_001264275", "EGF-containing fibulin-like extracellular matrix protein 2 isoform 3 precursor", "333", "" ], [ "A0A8I5ZQ10-1", "NP_001099351", "N-alpha-acetyltransferase 50 isoform 2", "168", "" ], [ "D3Z908-1", "NP_001100241", "ankyrin repeat domain-containing protein 24", "903", "" ], [ "A0A0G2K7F8-1", "NP_001128273", "apolipoprotein L3", "365", "" ], [ "A0A8I5ZRS3-1", "NP_001014161", "SLAIN motif-containing protein 1 isoform 3", "306", "" ], [ "Q5FAQ9-1", "NP_001007755", "ras association domain-containing protein 1 isoform 2", "270", "" ], [ "D3ZDS9-1", "NP_001258245", "interferon alpha/beta receptor 1 isoform 2", "439", "" ], [ "A0A0G2K130-1", "NP_665731", "TRAF family member-associated NF-kappa-B activator isoform 1", "414", "" ], [ "Q53E76-1", "NP_001019445", "glycosyltransferase-like domain-containing protein 1 isoform 2", "389", "" ], [ "D3ZA60-1", "NP_001102701", "leucine-rich repeat-containing protein 61", "259", "" ], [ "D4A954-1", "NP_001243079", "Secreted seminal-vesicle Ly-6 protein 1-like precursor", "99", "" ], [ "Q5M7A3-1", "NP_001012126", "solute carrier family 35 member G2", "412", "" ], [ "Q5HZA2-1", "NP_001012046", "protein sprouty homolog 2", "314", "" ], [ "A0A096MJ01-1", "NP_001264094", "LIM domain-binding protein 3 isoform 1", "726", "" ], [ "A0A096MJ01-1", "NP_001264087", "LIM domain-binding protein 3 isoform 3", "288", "" ], [ "A0A8I6AKZ1-1", "NP_001128001", "BTB/POZ domain-containing protein KCTD17 isoform 2", "246", "" ], [ "A0A0G2JTZ7-1", "NP_001100292", "solute carrier family 35 member F2 isoform 2", "215", "" ], [ "D3ZVQ0-1", "NP_001100089", "ubiquitin carboxyl-terminal hydrolase 5 isoform 1", "858", "" ], [ "F1LPV0-1", "NP_001136421", "asparagine--tRNA ligase, cytoplasmic isoform 2", "507", "" ], [ "F1LPV0-1", "NP_001020806", "asparagine--tRNA ligase, cytoplasmic isoform 1", "558", "" ], [ "A0A0G2K350-1", "NP_001100854", "gamma-soluble NSF attachment protein isoform 2", "230", "" ], [ "A0A8I6A5Y0-1", "NP_001020811", "vacuolar protein sorting-associated protein VTA1 homolog isoform 2", "251", "" ], [ "D3ZW49-1", "NP_001099759", "transmembrane protein 9B isoform 2", "124", "" ], [ "A0A8I6AL43-1", "NP_001099770", "arginyl-tRNA--protein transferase 1 isoform 3", "509", "" ], [ "F1M784-1", "NP_001099838", "phosphoinositide 3-kinase adapter protein 1 isoform 2", "790", "" ] ] }, "readme": "Name\n - Rat Protein Information (NCBI RefSeq)\n\nVersion\n - v-2.2.1\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], 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-2.2.1/reviewed/rat_protein_xref_refseq.csv\n Name: refseq_protein_all_10116.gpff\n URI: https:/data.glygen.org/ln2downloads/ncbi/refseq/2023_10_12/refseq_protein_all_10116.gpff\n Output Subdomain\n Name: rat_protein_info_refseq.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/rat_protein_info_refseq.csv\n Name: rat_protein_info_refseq.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/rat_protein_info_refseq.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"14836\"\n Name: \"p_refseq_ac_best_match\"\n Description: \"Best match NCBI RefSeq protein accession to UniProtKB canonical accession\"\n Unique Values: \"17487\"\n Name: \"refseq_protein_name\"\n Description: \"Name of the protein in NCBI RefSeq database\"\n Unique Values: \"17452\"\n Name: \"refseq_protein_length\"\n Description: \"Length of the protein in NCBI RefSeq database\"\n Unique Values: \"1916\"\n Name: \"refseq_protein_summary\"\n Description: \"Function of the protein in NCBI RefSeq database\"\n Unique Values: \"162\"", "downloadurl": "/ln2data/releases/data/v-2.2.1/reviewed/rat_protein_info_refseq.csv" }