{ "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_036669" ], [ "Robel", " feat NP_036669" ], [ "P15393-1", "NP_036669", "cytochrome P450 11B1, mitochondrial precursor", "499", "catalyzes the conversion of 11-deoxycorticosterone to corticosterone [RGD, Feb 2006]. " ], [ "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_604456" ], [ "Robel", " feat NP_604456" ], [ "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]. " ], [ "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_001128560" ], [ "Robel", " feat NP_001128560" ], [ "A0A0G2KB91-1", "NP_001128560", "zinc finger protein 385A isoform 1", "415", "" ], [ "Robel", " mapped NP_001129365" ], [ "Robel", " feat NP_001129365" ], [ "A0A0G2K2C7-1", "NP_001129365", "probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform 1", "2547", "" ], [ "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_001020288" ], [ "Robel", " feat NP_001020288" ], [ "A0A8I5ZY32-1", "NP_001020288", "EH domain-binding protein 1-like protein 1 isoform 1", "774", "" ], [ "Robel", " mapped NP_001102477" ], [ "Robel", " feat NP_001102477" ], [ "A0A0G2K6W6-1", "NP_001102477", "DIS3-like exonuclease 2 isoform 1", "890", "" ], [ "Robel", " mapped NP_001102499" ], [ "Robel", " feat NP_001102499" ], [ "F1LYS7-1", "NP_001102499", "delta-sarcoglycan isoform a", "255", "" ], [ "Robel", " mapped NP_001029179" ], [ "Robel", " feat NP_001029179" ], [ "A0A8I6A3B1-1", "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_001072116" ], [ "Robel", " feat NP_001072116" ], [ "D3ZF56-1", "NP_001072116", "transmembrane protein 134 isoform b", "180", "" ], [ "Robel", " mapped NP_001009498" ], [ "Robel", " feat NP_001009498" ], [ "A0A0G2JUK7-1", "NP_001009498", "immunoreceptor Ly49si2", "267", "" ], [ "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_001264235" ], [ "Robel", " feat NP_001264235" ], [ "D3Z8G8-1", "NP_001264235", "MAU2 chromatid cohesion factor homolog isoform 2", "104", "" ], [ "Robel", " mapped NP_001292054" ], [ "Robel", " feat NP_001292054" ], [ "D4A2I6-1", "NP_001292054", "transmembrane protein 220 isoform 2", "94", "" ], [ "Robel", " mapped NP_001102013" ], [ "Robel", " feat NP_001102013" ], [ "D4A3E8-1", "NP_001102013", "28S ribosomal protein S27, mitochondrial isoform 2", "96", "" ], [ "Robel", " mapped NP_001012181" ], [ "Robel", " feat NP_001012181" ], [ "A6JV53-1", "NP_001012181", "ETS-related transcription factor Elf-2 isoform 2", "519", "" ], [ "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_001099376" ], [ "Robel", " feat NP_001099376" ], [ "M0R4X8-1", "NP_001099376", "SUMO-specific isopeptidase USPL1 isoform 2", "518", "" ], [ "Robel", " mapped NP_001128518" ], [ "Robel", " feat NP_001128518" ], [ "A0A0G2JVX9-1", "NP_001128518", "cAMP-regulated phosphoprotein 21 isoform 1", "88", "" ] ] }, "readme": "Name\n - Rat Protein Information (NCBI RefSeq)\n\nVersion\n - v-2.3.1\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-2.3.1/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-2.3.1/reviewed/rat_protein_info_refseq.csv\n Name: rat_protein_info_refseq.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/rat_protein_info_refseq.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"14029\"\n Name: \"p_refseq_ac_best_match\"\n Description: \"Best match NCBI RefSeq protein accession to UniProtKB canonical accession\"\n Unique Values: \"49221\"\n Name: \"refseq_protein_name\"\n Description: \"Name of the protein in NCBI RefSeq database\"\n Unique Values: \"16381\"\n Name: \"refseq_protein_length\"\n Description: \"Length of the protein in NCBI RefSeq database\"\n Unique Values: \"1864\"\n Name: \"refseq_protein_summary\"\n Description: \"Function of the protein in NCBI RefSeq database\"\n Unique Values: \"149\"", "downloadurl": "/ln2data/releases/data/v-2.3.1/reviewed/rat_protein_info_refseq.csv" }