{ "bcoid": "GLY_000267", "title": "Rat Gene Locus (Ensembl)", "description": "The Rat Gene Locus (Ensembl) contains rat [taxid:10116] UniProtKB canonical accessions mapped to the ...", "filename": "rat_protein_genelocus.csv", "filetype": "csv", "categories": { "species": [ "Rattus norvegicus" ], "molecule": [ "Protein" ], "tags": [ "Gene Coordinates" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "D3ZB44-1...", "Zfp324..." ], [ "D3ZB41-1...", "Zfp78..." ] ], "headers": [ "uniprotkb_ca...", "gene_symbol..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "gene_symbol" }, { "type": "string", "label": "ensembl_gene_id" }, { "type": "string", "label": "chromosome_id" }, { "type": "string", "label": "start_pos" }, { "type": "string", "label": "end_pos" }, { "type": "string", "label": "strand" } ], [ "D3ZB44-1", "Zfp324", "ENSRNOG00000027436", "1", "65606520", "65611815", "0" ], [ "D3ZB41-1", "Zfp78", "ENSRNOG00000015322", "1", "71183171", "71190423", "0" ], [ "D3ZB49-1", "Osgin2", "ENSRNOG00000009358", "5", "29663685", "29682005", "0" ], [ "D3ZB48-1", "Hook1", "ENSRNOG00000026226", "5", "114940053", "115000691", "1" ], [ "A0A0G2JVG5-1", "LOC102552378", "ENSRNOG00000030948", "12", "50211981", "50213400", "0" ], [ "P30938-1", "Sstr5", "ENSRNOG00000018834", "10", "14847749", "14853827", "0" ], [ "A0A096MJY4-1", "Mef2c", "ENSRNOG00000033134", "2", "11658568", "11822787", "1" ], [ "A0A096MJY7-1", "Lsm14a", "ENSRNOG00000021133", "1", "90200876", "90246297", "0" ], [ "A0A096MJY1-1", "Gpc6", "ENSRNOG00000046660", "15", "102164751", "103170847", "1" ], [ "A0A096MJY2-1", "Stoml3", "ENSRNOG00000011006", "2", "142717281", "142735410", "1" ], [ "A0A8J8XIU8-1", "Rbm39", "ENSRNOG00000019848", "3", "151691514", "151724654", "0" ], [ "P30937-1", "Sstr4", "ENSRNOG00000004641", "3", "142739781", "142741644", "1" ], [ "O35152-1", "Bet1l", "ENSRNOG00000013165", "1", "213602850", "213605643", "0" ], [ "P30936-1", "Sstr3", "ENSRNOG00000007332", "7", "119760888", "119768082", "0" ], [ "O35158-1", "Cdon", "ENSRNOG00000011789", "8", "36625733", "36710949", "1" ], [ "F7FI04-1", "Snx10", "ENSRNOG00000011944", "4", "81311490", "81374158", "1" ], [ "Q9QYH1-1", "Mpp4", "ENSRNOG00000010486", "9", "65917917", "65957101", "0" ], [ "P02764-1", "Orm1", "ENSRNOG00000007886", "5", "79179417", "79182820", "1" ], [ "P02767-1", "Ttr", "ENSRNOG00000016275", "18", "15532963", "15540177", "0" ], [ "D4A4W8-1", "Tbxt", "ENSRNOG00000012229", "1", "52887067", "52894832", "0" ], [ "D4A4W1-1", "Fam174b", "ENSRNOG00000012369", "1", "135083974", "135162685", "1" ], [ "D4A4W2-1", "Slc47a2", "ENSRNOG00000038055", "10", "47588497", "47630799", "0" ], [ "F7EN52-1", "Cyp46a1", "ENSRNOG00000007147", "6", "132242328", "132273787", "1" ], [ "D4A4W4-1", "Ephx3", "ENSRNOG00000027319", "7", "14212470", "14217778", "0" ], [ "D4A4W5-1", "Atp10b", "ENSRNOG00000003781", "10", "28449335", "28864255", "1" ], [ "D4A4W6-1", "Slirp", "ENSRNOG00000012314", "6", "111476768", "111486039", "1" ], [ "D4A4W7-1", "Mgarp", "ENSRNOG00000011923", "2", "140444965", "140453107", "0" ], [ "G3V6I6-1", "Adipor1", "ENSRNOG00000004143", "13", "51240911", "51260228", "1" ], [ "P39020-1", "Meox2", "ENSRNOG00000006588", "6", "56625650", "56689238", "1" ], [ "Q0HA29-1", "Nmnat2", "ENSRNOG00000027697", "13", "70379346", "70559458", "1" ], [ "A0A0G2K0T8-1", "Fam25a", "ENSRNOG00000055025", "16", "10702263", "10706073", "0" ], [ "A0A8I6AEL0-1", "Map3k5", "ENSRNOG00000031700", "1", "15412603", "15613746", "1" ], [ "A0A096MJK8-1", "Slfn2", "ENSRNOG00000037113", "10", "70370300", "70376331", "1" ], [ "A0A8I6AEL5-1", "Arid5b", "ENSRNOG00000000635", "20", "21564975", "21880715", "1" ], [ "P01237-1", "Prl", "ENSRNOG00000017374", "17", "39814244", "39824299", "0" ], [ "A0A8I6AEL7-1", "AABR07038788.1", "ENSRNOG00000029559", "X", "60761567", "60763583", "1" ], [ "P01230-1", "Lhb", "ENSRNOG00000047040", "1", "101410019", "101413724", "1" ], [ "M0RB75-1", "Kdm4b", "ENSRNOG00000049221", "9", "10653216", "10734073", "0" ], [ "M0RB79-1", "RGD1562667", "ENSRNOG00000045888", "10", "104932616", "104935917", "1" ], [ "Q9JHY8-1", "Lig1", "ENSRNOG00000014193", "1", "75356220", "75394758", "1" ], [ "Q9JHY1-1", "F11r", "ENSRNOG00000004414", "13", "89826254", "89850612", "1" ], [ "Q9JHY2-1", "Sfxn3", "ENSRNOG00000015442", "1", "264796812", "264805157", "1" ], [ "Q9JHY7-1", "Birc5", "ENSRNOG00000050819", "10", "106856097", "106864413", "1" ], [ "Q9EQZ1-1", "Tsc22d3", "ENSRNOG00000056135", "X", "111884295", "111887906", "0" ], [ "F1MAA4-1", "Atp13a2", "ENSRNOG00000008052", "5", "159512285", "159531637", "1" ], [ "Q99JD4-1", "Clasp2", "ENSRNOG00000009161", "8", "122003916", "122185495", "1" ], [ "A0A8I6ADP7-1", "Acer3", "ENSRNOG00000036866", "1", "163160979", "163263606", "0" ], [ "Q99JD1-1", "Defb22", "ENSRNOG00000007525", "3", "147961818", "147966097", "0" ], [ "Q99JD3-1", "Slc25a21", "ENSRNOG00000008931", "6", "77624385", "77848434", "0" ], [ "Q99JD2-1", "Tekt1", "ENSRNOG00000014973", "10", "58895674", "58924137", "0" ], [ "A0A8I5Y6V4-1", "Msantd1", "ENSRNOG00000010867", "14", "81090858", "81100803", "0" ], [ "Q02294-1", "Cacna1b", "ENSRNOG00000004560", "3", "1740024", "1924827", "0" ], [ "Q02293-1", "Fntb", "ENSRNOG00000007660", "6", "99883959", "99966988", "1" ], [ "A0A8I5Y1B9-1", "Zfp949", "ENSRNOG00000043223", "8", "96356088", "96380770", "1" ], [ "D3ZGR6-1", "Ccdc138", "ENSRNOG00000028581", "20", "28078500", "28157071", "1" ], [ "D3ZGR7-1", "Trir", "ENSRNOG00000003863", "19", "26142720", "26146136", "1" ], [ "A0A8I6ABF2-1", "Lmf1", "ENSRNOG00000000230", "10", "14945265", "15031942", "1" ], [ "A0A8I6ABF4-1", "AABR07018058.1", "ENSRNOG00000057750", "15", "37710848", "37711222", "0" ], [ "Q8K5E0-1", "Lpar3", "ENSRNOG00000015260", "2", "252090669", "252159903", "1" ], [ "Q460M5-1", "Lrfn2", "ENSRNOG00000011803", "9", "13845757", "13877130", "0" ], [ "Q9R1N3-1", "Slc4a7", "ENSRNOG00000005957", "15", "11836286", "11912916", "0" ], [ "D3ZIY3-1", "Ythdf3", "ENSRNOG00000010084", "2", "100677411", "100710417", "1" ], [ "D3ZSP7-1", "Ttc3", "ENSRNOG00000001682", "11", "34598492", "34738791", "1" ], [ "P48550-1", "Kcnj6", "ENSRNOG00000001658", "11", "35024196", "35099383", "0" ], [ "D3ZFP5-1", "LOC691352", "ENSRNOG00000038422", "10", "44238354", "44243402", "0" ], [ "D3ZFP4-1", "Mcm3", "ENSRNOG00000012543", "9", "26914057", "26932201", "0" ], [ "D3ZFP7-1", "Insc", "ENSRNOG00000024712", "1", "184299250", "184407480", "1" ], [ "D3ZFP6-1", "Ticrr", "ENSRNOG00000015520", "1", "141391262", "141433109", "1" ], [ "D3ZYL2-1", "Kiaa0408L", "ENSRNOG00000042309", "1", "31040142", "31055453", "0" ], [ "D3ZYL0-1", "Ripk1", "ENSRNOG00000017787", "17", "31537591", "31569904", "0" ], [ "Q6B4M5-1", "Pard6a", "ENSRNOG00000017746", "19", "37668133", "37672729", "1" ], [ "D4A131-1", "Mrpl4", "ENSRNOG00000020659", "8", "22021213", "22027228", "1" ], [ "D4A138-1", "Nanos3", "ENSRNOG00000031593", "19", "25284909", "25288335", "0" ], [ "A0A8I6A326-1", "Rbm6", "ENSRNOG00000018333", "8", "116535403", "116635851", "0" ], [ "D3ZCS5-1", "Eme1", "ENSRNOG00000024420", "10", "82367084", "82374171", "0" ], [ "D3ZCS4-1", "Iqgap3", "ENSRNOG00000027894", "2", "187447501", "187489630", "1" ], [ "D3ZHE2-1", "Yipf7", "ENSRNOG00000002224", "14", "62567745", "62595854", "0" ], [ "D3ZHE3-1", "Zswim9", "ENSRNOG00000014186", "1", "75335894", "75354820", "0" ], [ "D3ZCS1-1", "Rgs13", "ENSRNOG00000003888", "13", "60970247", "61003744", "0" ], [ "D3ZHE5-1", "Rab11fip4", "ENSRNOG00000014135", "10", "66942398", "67048308", "1" ], [ "Q9JIL8-1", "Rad50", "ENSRNOG00000033065", "10", "39001498", "39054142", "0" ], [ "D3ZCS9-1", "RGD1309350", "ENSRNOG00000048275", "1", "213577122", "213580542", "1" ], [ "O88664-1", "Taok1", "ENSRNOG00000015692", "10", "62566732", "62630155", "1" ], [ "A0A8I5ZRG3-1", "Frmd4b", "ENSRNOG00000007764", "4", "129658840", "129846642", "0" ] ] }, "readme": "Name\n - Rat Gene Locus (Ensembl)\n\nVersion\n - v-2.1.1\n\nCreated on\n - 2019-09-06T14:06:38.993695\n\nModified on\n - 2022-09-26T09:04:48.000439\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 - Maria Martin [martin@ebi.ac.uk], Preethi Vasudev [pvasudev@ebi.ac.uk]\n\nChecksum\n - \n\nUsability Domain\n - The Rat Gene Locus (Ensembl) contains rat [taxid:10116] UniProtKB canonical accessions mapped to the corresponding ENSEMBL Gene ID, chromosome ID along with the gene's start and end position on the chromosome. The dataset is derived from 2019-09 UniProt release. The dataset is contributed by EMBL-EBI-UniProtKB and processed by GlyGen. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen\n\nDescription Domain\n Keywords\n - gene coordinates\n - start position\n - end position\n - Ensembl\n - strand\n\n Pipeline Steps\n - Step-1: The script loads the UniProtKB canonical accessions that are mapped to ENSEMBL Gene identifiers from the triplestore containing triples from nt file and extracts the data as a csv dataset\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_masterlist.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/rat_protein_masterlist.csv\n Name: Rattus_norvegicus.Rnor_6.0.95.gtf\n URI: /data/shared/glyds/downloads/ucsc/gtf/Rattus_norvegicus.Rnor_6.0.95.gtf\n Output Subdomain\n Name: rat_protein_genelocus.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/rat_protein_genelocus.csv\n Name: rat_protein_genelocus.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/rat_protein_genelocus.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"17195\"\n Name: \"gene_symbol\"\n Description: \"\"Official gene name/symbol assigned to the gene. Human gene names/symbols are approved by the HUGO Gene Nomenclature Committee (HGNC)\"\n Unique Values: \"17177\"\n Name: \"ensembl_gene_id\"\n Description: \"Gene Identifier in Ensembl database\"\n Unique Values: \"17177\"\n Name: \"chromosome_id\"\n Description: \"Chromosome number identifier\"\n Unique Values: \"49\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"17171\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"17176\"\n Name: \"strand\"\n Description: \"The strand of the gene\"\n Unique Values: \"2\"", "downloadurl": "/ln2data/releases/data/v-2.1.1/reviewed/rat_protein_genelocus.csv" }