{ "bcoid": "GLY_000135", "title": "Human Transcript Locus (Ensembl Transcript coordinates)", "description": "The Human Transcript Locus (Ensembl Transcript coordinates)s contains UniProtKB human [taxid:9606] canonical ...", "filename": "human_protein_transcriptlocus.csv", "filetype": "csv", "categories": { "species": "Homo sapiens", "molecule": "Protein", "tags": "Transcript Coordinates", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "Q9Y6C9-1...", "E9PIE4-1..." ], [ "Q9Y6C9-1...", "Q9Y6C9-1..." ] ], "headers": [ "uniprotkb_ca...", "uniprotkb_is..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "uniprotkb_isoform_ac" }, { "type": "string", "label": "transcript_id" }, { "type": "string", "label": "peptide_id" }, { "type": "string", "label": "chromosome_id" }, { "type": "string", "label": "start_pos" }, { "type": "string", "label": "end_pos" }, { "type": "string", "label": "strand" } ], [ "Q9Y6C9-1", "E9PIE4-1", "ENST00000530428", "ENSP00000432043", "11", "47642465", "47622713", "1" ], [ "Q9Y6C9-1", "Q9Y6C9-1", "ENST00000302503", "ENSP00000303222", "11", "47642465", "47618836", "1" ], [ "P30613-1", "P30613-1", "ENST00000342741", "ENSP00000339933", "1", "155301395", "155290575", "1" ], [ "P30613-1", "P30613-2", "ENST00000571194", "ENSP00000461487", "1", "155316291", "155305979", "1" ], [ "P30613-1", "A0A0G2JLC7-1", "ENST00000573938", "ENSP00000459447", "1", "155316360", "155315552", "1" ], [ "P30613-1", "F8W6W2-1", "ENST00000434082", "ENSP00000398037", "1", "155300188", "155295135", "1" ], [ "Q5MIZ7-1", "Q5MIZ7-1", "ENST00000616407", "ENSP00000483228", "2", "55617285", "55549914", "1" ], [ "Q5MIZ7-1", "Q5MIZ7-2", "ENST00000616288", "ENSP00000484116", "2", "55617285", "55549914", "1" ], [ "Q5MIZ7-1", "Q5MIZ7-3", "ENST00000611717", "ENSP00000478677", "2", "55617285", "55549914", "1" ], [ "A0A1W2PQ27-1", "A0A1W2PQ27-1", "ENST00000524542", "ENSP00000491894", "11", "4339244", "4338663", "1" ], [ "P51788-1", "A0A1B0GVL9-1", "ENST00000637909", "ENSP00000490570", "3", "184358741", "184355755", "1" ], [ "P51788-1", "A0A1B0GVU4-1", "ENST00000638134", "ENSP00000490659", "3", "184361444", "184357055", "1" ], [ "P51788-1", "A0A1B0GUY6-1", "ENST00000636241", "ENSP00000490299", "3", "184361448", "184354290", "1" ], [ "P51788-1", "H7C0Q8-1", "ENST00000430397", "ENSP00000396231", "3", "184357020", "184354290", "1" ], [ "P51788-1", "A0A1B0GVW7-1", "ENST00000637538", "ENSP00000490682", "3", "184357697", "184354290", "1" ], [ "P51788-1", "A0A1B0GTY0-1", "ENST00000475279", "ENSP00000489885", "3", "184358049", "184357055", "1" ], [ "P51788-1", "P51788-1", "ENST00000265593", "ENSP00000265593", "3", "184361479", "184346609", "1" ], [ "P51788-1", "P51788-3", "ENST00000344937", "ENSP00000345056", "3", "184361479", "184346609", "1" ], [ "P51788-1", "P51788-4", "ENST00000434054", "ENSP00000400425", "3", "184361479", "184346609", "1" ], [ "P51788-1", "P51788-5", "ENST00000457512", "ENSP00000391928", "3", "184361479", "184346609", "1" ], [ "P51788-1", "A0A1B0GTJ3-1", "ENST00000636419", "ENSP00000489724", "3", "184354959", "184354189", "1" ], [ "P51788-1", "A0A1B0GUZ8-1", "ENST00000636492", "ENSP00000490313", "3", "184359107", "184354310", "1" ], [ "P51788-1", "A0A1B0GWC8-1", "ENST00000636658", "ENSP00000490875", "3", "184357696", "184355496", "1" ], [ "P51788-1", "A0A1B0GV52-1", "ENST00000636180", "ENSP00000490374", "3", "184361479", "184357057", "1" ], [ "P23919-1", "H7BZ20-1", "ENST00000420144", "ENSP00000387379", "2", "241685877", "241676178", "1" ], [ "P23919-1", "H7C3A4-1", "ENST00000432348", "ENSP00000410647", "2", "241686742", "241682229", "1" ], [ "P23919-1", "H7C312-1", "ENST00000445261", "ENSP00000408939", "2", "241686712", "241676128", "1" ], [ "P23919-1", "P23919-1", "ENST00000305784", "ENSP00000304802", "2", "241686783", "241676130", "1" ], [ "P23919-1", "G5E9E9-1", "ENST00000400770", "ENSP00000383581", "2", "241686783", "241678640", "1" ], [ "Q8NHX4-1", "A0A087WU50-1", "ENST00000612823", "ENSP00000478372", "2", "230996234", "231002786", "0" ], [ "Q8NHX4-1", "H7C3E6-1", "ENST00000423134", "ENSP00000411374", "2", "230996389", "231002798", "0" ], [ "Q8NHX4-1", "H7C283-1", "ENST00000440792", "ENSP00000404510", "2", "230996336", "231002796", "0" ], [ "Q8NHX4-1", "F8WDD9-1", "ENST00000454918", "ENSP00000395644", "2", "230996234", "231000453", "0" ], [ "Q8NHX4-1", "Q8NHX4-1", "ENST00000433428", "ENSP00000403804", "2", "230996234", "231002786", "0" ], [ "Q8NHX4-1", "A0A2R8Y5R0-1", "ENST00000645363", "ENSP00000494655", "2", "230990324", "231002786", "0" ], [ "Q8NHX9-1", "Q8NHX9-1", "ENST00000294309", "ENSP00000294309", "11", "69048998", "69087950", "0" ], [ "Q8NHX9-1", "A0A1B0GTM1-1", "ENST00000635811", "ENSP00000490341", "11", "69048998", "69085250", "0" ], [ "Q8NHX9-1", "A0A1B0GUM5-1", "ENST00000637342", "ENSP00000490171", "11", "69048998", "69135525", "0" ], [ "Q8NHX9-1", "E7ETX0-1", "ENST00000542467", "ENSP00000445551", "11", "69048998", "69087950", "0" ], [ "Q9NXR8-1", "Q9NXR8-1", "ENST00000315870", "ENSP00000320566", "7", "120950897", "120974841", "0" ], [ "Q9NXR8-1", "Q9NXR8-2", "ENST00000339121", "ENSP00000341697", "7", "120950897", "120956168", "0" ], [ "Q9NXR8-1", "Q9NXR8-3", "ENST00000427726", "ENSP00000410406", "7", "120950897", "120966637", "0" ], [ "Q9NXR8-1", "E7ET07-1", "ENST00000431467", "ENSP00000388506", "7", "120951181", "120974841", "0" ], [ "Q9NXR8-1", "A0A0C4DG38-1", "ENST00000445699", "ENSP00000395719", "7", "120950897", "120955654", "0" ], [ "Q9C0H5-1", "Q9C0H5-1", "ENST00000276826", "ENSP00000276826", "8", "144605614", "144530425", "1" ], [ "Q9C0H5-1", "Q9C0H5-2", "ENST00000377307", "ENSP00000366522", "8", "144605614", "144530425", "1" ], [ "Q9NXR1-2", "Q9NXR1-2", "ENST00000396355", "ENSP00000379643", "16", "15664779", "15724248", "0" ], [ "Q07960-1", "H0YE29-1", "ENST00000528837", "ENSP00000434883", "11", "46696099", "46679217", "1" ], [ "Q07960-1", "E9PNR6-1", "ENST00000525488", "ENSP00000432794", "11", "46696107", "46681070", "1" ], [ "Q07960-1", "Q07960-1", "ENST00000311956", "ENSP00000310491", "11", "46696107", "46679040", "1" ], [ "Q9NXR5-1", "S4R3R2-1", "ENST00000603993", "ENSP00000474638", "13", "110893132", "110883536", "1" ], [ "Q9NXR5-1", "Q9NXR5-1", "ENST00000267339", "ENSP00000267339", "13", "110914934", "110879640", "1" ], [ "Q9NXR5-1", "Q9NXR5-2", "ENST00000310847", "ENSP00000312534", "13", "110914934", "110893153", "1" ], [ "Q9NXR5-1", "Q8IUW1-1", "ENST00000465753", "ENSP00000431927", "13", "110914934", "110900634", "1" ], [ "Q9NXR7-2", "Q9NXR7-1", "ENST00000344773", "ENSP00000343412", "2", "27894557", "28327430", "0" ], [ "Q9NXR7-2", "Q9NXR7-2", "ENST00000342045", "ENSP00000339371", "2", "27894557", "28338510", "0" ], [ "Q9NXR7-2", "Q9NXR7-4", "ENST00000361704", "ENSP00000354699", "2", "27894557", "28310121", "0" ], [ "Q96J66-1", "Q96J66-1", "ENST00000394748", "ENSP00000378231", "16", "48231921", "48167277", "1" ], [ "Q96J66-1", "Q96J66-2", "ENST00000353782", "ENSP00000311326", "16", "48231921", "48167277", "1" ], [ "Q96J66-1", "H3BRJ2-1", "ENST00000569991", "ENSP00000456268", "16", "48231921", "48224348", "1" ], [ "P40424-1", "P40424-2", "ENST00000367897", "ENSP00000356872", "1", "164559823", "164821580", "0" ], [ "P40424-1", "P40424-3", "ENST00000627490", "ENSP00000485692", "1", "164559823", "164849399", "0" ], [ "P40424-1", "H0YLF5-1", "ENST00000559240", "ENSP00000453188", "1", "164559823", "164846673", "0" ], [ "P40424-1", "S4R377-1", "ENST00000485769", "ENSP00000473998", "1", "164559823", "164560164", "0" ], [ "P40424-1", "H0YLD4-1", "ENST00000482110", "ENSP00000453163", "1", "164792544", "164799887", "0" ], [ "P40424-1", "F8WA05-1", "ENST00000340699", "ENSP00000341455", "1", "164559823", "164792738", "0" ], [ "P40424-1", "A0A0A0MTI0-1", "ENST00000540236", "ENSP00000439943", "1", "164792493", "164846673", "0" ], [ "P40424-1", "H0YKH1-1", "ENST00000559578", "ENSP00000452804", "1", "164563263", "164799881", "0" ], [ "P40424-1", "P40424-1", "ENST00000420696", "ENSP00000405890", "1", "164559823", "164846673", "0" ], [ "P40424-1", "H0YLM3-1", "ENST00000559560", "ENSP00000453262", "1", "164792544", "164799794", "0" ], [ "P40424-1", "A0A087X0P4-1", "ENST00000612123", "ENSP00000483563", "1", "164792493", "164821580", "0" ], [ "P40424-1", "H0YLT4-1", "ENST00000558837", "ENSP00000453331", "1", "164792544", "164807569", "0" ], [ "P40424-1", "H0YLB0-1", "ENST00000560641", "ENSP00000452727", "1", "164792544", "164846673", "0" ], [ "P40425-1", "P40425-1", "ENST00000453961", "ENSP00000397177", "6", "32138383", "32134853", "1" ], [ "P40426-1", "H0Y5D0-1", "ENST00000428092", "ENSP00000397903", "9", "125865271", "125935531", "0" ], [ "P40426-1", "P40426-1", "ENST00000373489", "ENSP00000362588", "9", "125747454", "125965920", "0" ], [ "P40426-1", "U3KQA2-1", "ENST00000491787", "ENSP00000475679", "9", "125748575", "125929843", "0" ], [ "P40426-1", "H3BLX0-1", "ENST00000373492", "ENSP00000362591", "9", "125747454", "125929659", "0" ], [ "P40426-1", "P40426-2", "ENST00000342287", "ENSP00000341990", "9", "125747454", "125963055", "0" ], [ "P40426-1", "P40426-5", "ENST00000447726", "ENSP00000387456", "9", "125748575", "125965920", "0" ], [ "P40426-1", "Q5JS98-1", "ENST00000373487", "ENSP00000362586", "9", "125747454", "125965920", "0" ], [ "Q9H2I8-1", "A0A087WWI0-1", "ENST00000611255", "ENSP00000480240", "10", "75431725", "76557285", "0" ], [ "Q9H2I8-1", "A0A087WZZ7-1", "ENST00000611306", "ENSP00000482991", "10", "76036006", "76058789", "0" ], [ "Q9H2I8-1", "M0R2H0-1", "ENST00000496424", "ENSP00000472558", "10", "76319210", "76557285", "0" ] ] }, "readme": "Name\n - Human Transcript Locus (Ensembl Transcript coordinates)\n\nVersion\n - 1.5.30\n\nCreated on\n - 2019-03-16T16:05:08.939322\n\nModified on\n - 2020-04-10T11:41:42.489298\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Xavier Holmes [xavierh@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 Human Transcript Locus (Ensembl Transcript coordinates)s contains UniProtKB human [taxid:9606] canonical accessions mapped to their isoforms with further mapping to the corresponding ENSEMBL Transcript ID, Peptide ID, chromosome ID along with the transcripts's start and end position The dataset is derived from 2019-09 UniProtKB release. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen\n\nDescription Domain\n Keywords\n - transcript locus\n - ensembl transcript id\n - ensembl peptide id\n - chromosome\n - Ensembl\n\n Pipeline Steps\n - Step-1: The script loads the UniProtKB accessions that are mapped to UniProtKB isoforms and ENSEMBL Transcript and Peptide identifiers from the triplestore containing triples from nt file and maps it to the UniProtKB canonical accession to finally extract the data as a csv dataset\n\nExecution Domain\n Scripts - https://github.com/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/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: uniprot-proteome-homo-sapiens.nt\n URI: https://data.glygen.org/ln2data/releases/data/v-1.5.30/source/uniprot-proteome-homo-sapiens.nt\n Name: human_protein_masterlist.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.5.30/reviewed/human_protein_masterlist.csv\n Output Subdomain\n Name: human_protein_transcriptlocus.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.5.30/reviewed/human_protein_transcriptlocus.csv\n Name: human_protein_transcriptlocus.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.5.30/reviewed/human_protein_transcriptlocus.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"Accession assigned to the protein isoform chosen to be the canonical sequence to which all positional annotation refers in UniProtKB database\"\n Unique Values: \"19531\"\n Name: \"chromosome_id\"\n Description: \"Chromosome number identifier\"\n Unique Values: \"69\"\n Name: \"peptide_id\"\n Description: \"Protein identifier in Ensembl database\"\n Unique Values: \"84796\"\n Name: \"uniprotkb_isoform_ac\"\n Description: \"UniProtKB isoform that includes the canonical accession and other isoforms generated by alternative splicing\n Unique Values: \"84840\"\n Name: \"transcript_id\"\n Description: \"Transcript Identifier in Ensembl database\"\n Unique Values: \"84796\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"43934\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"64269\"\n Name: \"strand\"\n Description: \"The strand of the gene\"\n Unique Values: \"2\"", "downloadurl": "/ln2data/releases/data/v-1.5.30/reviewed/human_protein_transcriptlocus.csv" }