{ "bcoid": "GLY_000022", "title": "Mouse Protein Information (NCBI RefSeq)", "description": "The Mouse Protein Information (NCBI RefSeq) dataset contains mouse [taxid:10090] protein information ...", "filename": "mouse_protein_info_refseq.csv", "filetype": "csv", "categories": { "species": [ "Mus musculus" ], "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_001230020" ], [ "Robel", " feat NP_001230020" ], [ "J3KMM7-1", "NP_001230020", "uncharacterized protein LOC381272 isoform 2", "78", "" ], [ "Robel", " mapped NP_001153406" ], [ "Robel", " feat NP_001153406" ], [ "Q8VI97-1", "NP_001153406", "2'-5' oligoadenylate synthetase 1H isoform 2", "239", "" ], [ "Robel", " mapped NP_001177947" ], [ "Robel", " feat NP_001177947" ], [ "J3QNX6-1", "NP_001177947", "keratin associated protein 22-2", "67", "" ], [ "Robel", " mapped NP_034603" ], [ "Robel", " feat NP_034603" ], [ "G5E8J6-1", "NP_034603", "sarcoplasmic reticulum histidine-rich calcium-binding protein precursor", "738", "" ], [ "Robel", " mapped NP_663458" ], [ "Robel", " feat NP_663458" ], [ "E9Q459-1", "NP_663458", "zinc finger protein 160", "650", "" ], [ "Robel", " mapped NP_001161011" ], [ "Robel", " feat NP_001161011" ], [ "E9Q373-1", "NP_001161011", "vomeronasal 1 receptor, 238", "306", "" ], [ "Robel", " mapped NP_001186261" ], [ "Robel", " feat NP_001186261" ], [ "J3QPZ4-1", "NP_001186261", "uncharacterized protein LOC100041550", "227", "" ], [ "Robel", " mapped NP_660135" ], [ "Robel", " feat NP_660135" ], [ "Q14AZ4-1", "NP_660135", "2'-5'oligoadenylate synthetase 1F", "364", "" ], [ "Robel", " mapped NP_808591" ], [ "Robel", " feat NP_808591" ], [ "Q85ZW9-1", "NP_808591", "histocompatibility 2, M region locus 10.2 precursor", "329", "" ], [ "Robel", " mapped NP_001257418" ], [ "Robel", " feat NP_001257418" ], [ "G3UYD9-1", "NP_001257418", "uncharacterized protein LOC100502736", "124", "" ], [ "Robel", " mapped NP_001243238" ], [ "Robel", " feat NP_001243238" ], [ "J3QPC1-1", "NP_001243238", "uncharacterized protein LOC381043 precursor", "141", "" ], [ "Robel", " mapped NP_001153608" ], [ "Robel", " feat NP_001153608" ], [ "Q62457-1", "NP_001153608", "uncharacterized protein LOC100042428", "227", "" ], [ "Robel", " mapped NP_001153609" ], [ "Robel", " feat NP_001153609" ], [ "Q62458-1", "NP_001153609", "uncharacterized protein LOC100039614", "227", "" ], [ "Robel", " mapped NP_001013390" ], [ "Robel", " feat NP_001013390" ], [ "P0CB42-1", "NP_001013390", "neural regeneration protein", "135", "" ], [ "Robel", " mapped NP_001032835" ], [ "Robel", " feat NP_001032835" ], [ "G3UXL2-1", "NP_001032835", "ribose-phosphate pyrophosphokinase", "318", "" ], [ "Robel", " mapped NP_001291196" ], [ "Robel", " feat NP_001291196" ], [ "E9Q8G3-1", "NP_001291196", "transmembrane protein 265", "109", "" ], [ "Robel", " mapped NP_067420" ], [ "Robel", " feat NP_067420" ], [ "Q9ET52-1", "NP_067420", "cathepsin 6 precursor", "334", "" ], [ "Robel", " mapped NP_536684" ], [ "Robel", " feat NP_536684" ], [ "Q8CGV4-1", "NP_536684", "retinol dehydrogenase 16 precursor", "317", "" ], [ "Robel", " mapped NP_038572" ], [ "Robel", " feat NP_038572" ], [ "O19443-1", "NP_038572", "histocompatibility 2, M region locus 10.1 isoform 1 precursor", "331", "" ], [ "Robel", " mapped NP_001077424" ], [ "Robel", " feat NP_001077424" ], [ "P01942-1", "NP_001077424", "hemoglobin alpha, adult chain 2", "142", "" ], [ "Robel", " mapped NP_001161040" ], [ "Robel", " feat NP_001161040" ], [ "Q9EPT1-1", "NP_001161040", "vomeronasal 1 receptor Vmn1r187", "300", "" ], [ "Robel", " mapped NP_001161039" ], [ "Robel", " feat NP_001161039" ], [ "Q8R2C0-1", "NP_001161039", "vomeronasal 1 receptor Vmn1r186", "300", "" ], [ "Robel", " mapped NP_058652" ], [ "Robel", " feat NP_058652" ], [ "P02089-1", "NP_058652", "hemoglobin subunit beta-2", "147", "This gene encodes a beta polypeptide chain found in adult hemoglobin, which consists of a tetramer of two alpha chains and two beta chains, and which functions in the transport of oxygen to various peripheral tissues. This gene is one of a cluster of beta-hemoglobin genes that are distally regulated by a locus control region, and which are organized along the chromosome in the order of their developmental expression. In mouse, two major strain-specific haplotypes of the beta-globin gene cluster are found - a 'single' haplotype found in C57BL/-type strains, which includes two highly similar adult beta-globin genes, beta s and beta t, and a 'diffuse' haplotype found in strains such as BALB/c and 129Sv, which includes two somewhat diverse adult beta-globin genes, beta-major and beta-minor. This gene represents the beta-minor adult gene found in the 'diffuse' haplotype. Primary chromosome 7 of the mouse reference genome assembly, which is derived from C57BL/6 strain mice, represents the 'single' haplotype, while the 'diffuse' haplotype is represented in the reference genome collection by the BALB/c strain alternate contig, NT_095534.1. [provided by RefSeq, May 2013]. " ], [ "Robel", " mapped NP_001230019" ], [ "Robel", " feat NP_001230019" ], [ "J3KMM7-1", "NP_001230019", "uncharacterized protein LOC381272 isoform 1", "116", "" ], [ "Robel", " mapped NP_001243240" ], [ "Robel", " feat NP_001243240" ], [ "J3QMS9-1", "NP_001243240", "uncharacterized protein LOC381994", "113", "" ], [ "Robel", " mapped NP_001268445" ], [ "Robel", " feat NP_001268445" ], [ "G3UY31-1", "NP_001268445", "spermatogenesis associated glutamate (E)-rich protein-like", "267", "" ], [ "Robel", " mapped NP_001182020" ], [ "Robel", " feat NP_001182020" ], [ "J3QPU5-1", "NP_001182020", "coiled-coil domain-containing glutamate-rich protein 2 precursor", "274", "" ], [ "Robel", " mapped NP_001334487" ], [ "Robel", " feat NP_001334487" ], [ "A0A1B0GSA0-1", "NP_001334487", "keratin-associated protein 5-4-like", "219", "" ] ] }, "readme": "Name\n - Mouse Protein Information (NCBI RefSeq)\n\nVersion\n - v-2.3.1\n\nCreated on\n - 2019-01-23T17:21:05.888176\n\nModified on\n - 2022-09-26T08:48:18.844146\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 - Not Applicable []\n\nChecksum\n - \n\nUsability Domain\n - The Mouse Protein Information (NCBI RefSeq) dataset contains mouse [taxid:10090] 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 - protein summary\n - NCBI RefSeq\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: mouse_protein_xref_refseq.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/mouse_protein_xref_refseq.csv\n Name: refseq_protein_all_10090.gpff\n URI: https:/data.glygen.org/ln2downloads/ncbi/refseq/2023_10_12/refseq_protein_all_10090.gpff\n Output Subdomain\n Name: mouse_protein_info_refseq.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/mouse_protein_info_refseq.csv\n Name: mouse_protein_info_refseq.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/mouse_protein_info_refseq.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"19614\"\n Name: \"p_refseq_ac_best_match\"\n Description: \"Best match NCBI RefSeq protein accession to UniProtKB canonical accession\"\n Unique Values: \"68316\"\n Name: \"refseq_protein_name\"\n Description: \"Name of the protein in NCBI RefSeq database\"\n Unique Values: \"22687\"\n Name: \"refseq_protein_length\"\n Description: \"Length of the protein in NCBI RefSeq database\"\n Unique Values: \"2195\"\n Name: \"refseq_protein_summary\"\n Description: \"Function of the protein in NCBI RefSeq database\"\n Unique Values: \"1283\"", "downloadurl": "/ln2data/releases/data/v-2.3.1/reviewed/mouse_protein_info_refseq.csv" }