{ "bcoid": "GLY_001014", "title": "Chicken Protein Signal Peptide", "description": "The Chicken Protein Signal Peptide dataset contains Gallus gallus [taxid:9031] signal peptide information ...", "filename_list": "chicken_protein_signalp_annotation.csv, chicken_protein_signalp_peptidesequences.fasta, chicken_protein_signalp_cleavedsequences.fasta, chicken_protein_signalp_fullsequences.fasta", "filename": "chicken_protein_signalp_annotation.csv", "filetype": "csv", "categories": { "species": [ "Gallus gallus" ], "molecule": [ "Protein" ], "tag": [ "Signal Peptide" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ], "file_category": [ "annotation", "sequence" ] }, "minitable": { "content": [ [ "A0A8V0YKZ0-1...", "CHGA..." ], [ "A0A8V1ANX6-1...", "SDK2..." ] ], "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": "uniprotkb_protein_recommended_name" }, { "type": "string", "label": "uniprotkb_protein_length" }, { "type": "string", "label": "uniprotkb_protein_signalp_length" }, { "type": "string", "label": "uniprotkb_protein_signalp_cleaved_length" }, { "type": "string", "label": "signalp_start_pos" }, { "type": "string", "label": "signalp_end_pos" }, { "type": "string", "label": "uniprotkb_protein_sequence" }, { "type": "string", "label": "uniprotkb_protein_signalp_sequence" }, { "type": "string", "label": "uniprotkb_protein_signalp_cleaved_sequence" }, { "type": "string", "label": "eco_id" }, { "type": "string", "label": "evidence" } ], [ "A0A8V0YKZ0-1", "CHGA", "Chromogranin-A", "493", "17", "476", "1", "17", "MSPRLLAVLLLAVPAISLPVTNEMNKGDTKVMKCIVEVISDTLSKPDPLPISEECLETLRGDERIISILRHQNLLKELQEIAAQDAFMKPTVMEKGPITRWRAQGLPVLTSGANERTQQQKKNSGFEDELSEVLESQNDENKQRDVARQRPEEEQPTASLAELAAQKTQQKEDVREERKNSLEVRDSRLQDASPGEKDDQDEAESNEIKDAEDAQGEVALDNHVDKDLGEDEQQQRGEGEEQRRGPRNSLELEEEGEQPSKQGQGQSKEEAAEERVEQEDDGEDAPGEEDPTEAERLLDLAEEDGEAEEMQEDDGNDDALGFGKDEQSSEEEEEQPRLLRRGRHRLEDEGMQTEEDTFQSRDAKSEEMEDESSREWEDSKRWNKMDELAKQLSSKKHMEENDSGEDPDRSMKMAFRSHKYDFSSPEEDVRRSWKHHSKEDSSEGFPLVPMPEEKKDEEGSANRRTEDQELESLAAIEAELERVAHKLHELRRG", "MSPRLLAVLLLAVPAIS", "LPVTNEMNKGDTKVMKCIVEVISDTLSKPDPLPISEECLETLRGDERIISILRHQNLLKELQEIAAQDAFMKPTVMEKGPITRWRAQGLPVLTSGANERTQQQKKNSGFEDELSEVLESQNDENKQRDVARQRPEEEQPTASLAELAAQKTQQKEDVREERKNSLEVRDSRLQDASPGEKDDQDEAESNEIKDAEDAQGEVALDNHVDKDLGEDEQQQRGEGEEQRRGPRNSLELEEEGEQPSKQGQGQSKEEAAEERVEQEDDGEDAPGEEDPTEAERLLDLAEEDGEAEEMQEDDGNDDALGFGKDEQSSEEEEEQPRLLRRGRHRLEDEGMQTEEDTFQSRDAKSEEMEDESSREWEDSKRWNKMDELAKQLSSKKHMEENDSGEDPDRSMKMAFRSHKYDFSSPEEDVRRSWKHHSKEDSSEGFPLVPMPEEKKDEEGSANRRTEDQELESLAAIEAELERVAHKLHELRRG", "ECO_0000256", "SignalP" ], [ "A0A8V1ANX6-1", "SDK2", "", "2199", "25", "2174", "1", "25", "MARPGSWGLLCAVVLALPGPPGAGAQDDVSPYFKTEPVRSQVHLEGNRLVLTCMAEGSWPLEFKWLHNSRELTKFSLEYRYMITSLDRTHAGFYRCIVRNRMGALLQRQTEVQVAYMGSFEDSETQQSVSHGEAAVIRAPRIASFPQPQVTWFRDGRKISPSSRIAITLENTLVILSTVAPDAGRYYVQAVNDKNGDNKTSQPITLTVANVGGPADPIAPTIIVPPRNTSVVAGTSEVTMECVANARPLIKLHIIWKKDGVPISSGISDYSRRLTILNPTLGDSGYYECEAVLRSSSVPAVAEGAYLSVLEPPQFVKEPERHITAEMEKVVAIPCQAKGVPPPDMAWYKDASLIHPEQLSRFQLLADGSLQISGLLPDDTGMFQCFARNAAGEVQTTTYLAVTSIAPNITRGPQDSTVIDGMSVILNCETSGAPRPAITWQKGERILASGSVQLPRFTLLESGSLLVSPAHLTDAGTYTCLATNSRGVDEASADLVVWARTRITDPPQDQSVIKGTKASMSCGVTHDPSVDVRYIWEKDGAPLGTESGPRLRLDETGTLHISQTWSGDIGTYTCKVLSAGGNDSRSAHLRVRQLPHAPESPVAVLSPLEKRAINLTWAKPFDGNSPLLRYLVEISENNAPWTVLLASVDPELTWVVVRGLVPARSYQFRLCAVNDVGRSQFSKDTERVSLPEEPPSAPPQNVIASGRTNQSIMIQWQPPPESHQNGVLKGYIIRYCLAGLPVGYQFKNITNADVNNLLLEDLIIWTNYEIEVAAYNSAGLGVYSMKVTEWTLQGVPTVPPGNVQTEATNSTTIRFTWNPPSPQFINGINQGYKLIAWEPEHEEEATVVTVRPNFQDSVHVGYVVGLKKFTEYLTSVLCFTTPGDGPRSPPQLVRTHEDVPGPVGHLSFSEILDTSLKVSWQEPLEKNGILTGYRISWEEYNRTNTRVTHYLPNVTLEYRVTGLTALTTYTIEVAAMTSKGQGQVSSSTISSGVPPELPGAPTNLGISNIGPRSVTLQFRPGYDGKTSISRWQVEAQVGQNGEAEEWGLVHQLANEPDTRSLEVPNLNPYTYYSFRMRQVNIVGTSPPSLPSRRIQTLQAPPDVAPANVTLRTASETSLWLRWMPLLEQEYNGNPDSVGYRIRYLRSDGRGRAVVHVIHDRVEREYTIEDLEEWTEYRVQVQAFNAIGSGPWSHLVLGRTRESVPSSGPSNVSAQATSSSSMLVRWSDIPEADCNGLILGYKVMYKEKDSEARAQFWLAEGNTSRSAQLTGLGKFMLYEIRVLAFTRIGDGVPSRPPILERTLDDVPGPPVGMLFPEVRTTSVRLIWQPPTAPNGIILAYQLTHRLNTTTANAAVSEVLGPSTRQYTATGLQPEATYLFSITAQTRKGWGEAAEALVVTTEKRDRPQPPSKPLVRQEDVRARSVLLSWEPGSDGLSPVRFYTVQTRELPSGEWALHPASISHNATAFVVDRLKPFTSYKFRVKATNDIGDSEYSEESESLTTLQAAPEEAPTILSVTPHTTTSVLIRWQPPSEDKINGILLGFRLRYRELLYDSLRGFTLHGIGNPGATWAELTPVYAVHNLSEVSLTQYELDNLSKHRRYEIRMSVYNAVGEGPPSPPQEVFVGEAVPTGAPQNVAVKAATATQLDVTWEPPPTESQNGDIQGYKIHFWEAQRQNESARVKTLFLPETGVKLKNLTGYTSYWVSIAAFNAAGDGPRSTPVTARTQQAAPSAPGSIRFSELTTTSVNVSWEPPPLPNGILEGYRLVYEPCMPVDGEGTAGASEGTRGGPGSASISAGVSKIVTVDVKGNSPLWMKVKDLAEGITYRFRIRAKTFAYGPDVEANITTGPGEGAPGPPGEPFISRYGSAITIHWTSGDPGQGPITRYVIEARPSDEGLWDILIKDIPKEVTSYTFSMDILKQGVSYDFRVIAVNDYGYGTPSTPSPSVSAQKANPFYEEWWFLVVIALVGLIFILLLVFVLIIRGQSKKYAKKSDSGNGSKANALTHGEMVSLDESSFPALELNNRRLSVKNSFCRKNGIYTRSPPRPSPGSLHYSDEDVTKYNDLIPAESSSLTEKPSEVSDSQGSDSEYEVDPAHQKAHSFVNHYISDPTYYNSWRRQQKGISRAQAYSYTESDSGEPDHTPLSNSTSTQQGSLFRPKASRTPTPQTPGNPPSQPGTLYRPPSSLAPGSRAPIAGFSSFV", "MARPGSWGLLCAVVLALPGPPGAGA", "QDDVSPYFKTEPVRSQVHLEGNRLVLTCMAEGSWPLEFKWLHNSRELTKFSLEYRYMITSLDRTHAGFYRCIVRNRMGALLQRQTEVQVAYMGSFEDSETQQSVSHGEAAVIRAPRIASFPQPQVTWFRDGRKISPSSRIAITLENTLVILSTVAPDAGRYYVQAVNDKNGDNKTSQPITLTVANVGGPADPIAPTIIVPPRNTSVVAGTSEVTMECVANARPLIKLHIIWKKDGVPISSGISDYSRRLTILNPTLGDSGYYECEAVLRSSSVPAVAEGAYLSVLEPPQFVKEPERHITAEMEKVVAIPCQAKGVPPPDMAWYKDASLIHPEQLSRFQLLADGSLQISGLLPDDTGMFQCFARNAAGEVQTTTYLAVTSIAPNITRGPQDSTVIDGMSVILNCETSGAPRPAITWQKGERILASGSVQLPRFTLLESGSLLVSPAHLTDAGTYTCLATNSRGVDEASADLVVWARTRITDPPQDQSVIKGTKASMSCGVTHDPSVDVRYIWEKDGAPLGTESGPRLRLDETGTLHISQTWSGDIGTYTCKVLSAGGNDSRSAHLRVRQLPHAPESPVAVLSPLEKRAINLTWAKPFDGNSPLLRYLVEISENNAPWTVLLASVDPELTWVVVRGLVPARSYQFRLCAVNDVGRSQFSKDTERVSLPEEPPSAPPQNVIASGRTNQSIMIQWQPPPESHQNGVLKGYIIRYCLAGLPVGYQFKNITNADVNNLLLEDLIIWTNYEIEVAAYNSAGLGVYSMKVTEWTLQGVPTVPPGNVQTEATNSTTIRFTWNPPSPQFINGINQGYKLIAWEPEHEEEATVVTVRPNFQDSVHVGYVVGLKKFTEYLTSVLCFTTPGDGPRSPPQLVRTHEDVPGPVGHLSFSEILDTSLKVSWQEPLEKNGILTGYRISWEEYNRTNTRVTHYLPNVTLEYRVTGLTALTTYTIEVAAMTSKGQGQVSSSTISSGVPPELPGAPTNLGISNIGPRSVTLQFRPGYDGKTSISRWQVEAQVGQNGEAEEWGLVHQLANEPDTRSLEVPNLNPYTYYSFRMRQVNIVGTSPPSLPSRRIQTLQAPPDVAPANVTLRTASETSLWLRWMPLLEQEYNGNPDSVGYRIRYLRSDGRGRAVVHVIHDRVEREYTIEDLEEWTEYRVQVQAFNAIGSGPWSHLVLGRTRESVPSSGPSNVSAQATSSSSMLVRWSDIPEADCNGLILGYKVMYKEKDSEARAQFWLAEGNTSRSAQLTGLGKFMLYEIRVLAFTRIGDGVPSRPPILERTLDDVPGPPVGMLFPEVRTTSVRLIWQPPTAPNGIILAYQLTHRLNTTTANAAVSEVLGPSTRQYTATGLQPEATYLFSITAQTRKGWGEAAEALVVTTEKRDRPQPPSKPLVRQEDVRARSVLLSWEPGSDGLSPVRFYTVQTRELPSGEWALHPASISHNATAFVVDRLKPFTSYKFRVKATNDIGDSEYSEESESLTTLQAAPEEAPTILSVTPHTTTSVLIRWQPPSEDKINGILLGFRLRYRELLYDSLRGFTLHGIGNPGATWAELTPVYAVHNLSEVSLTQYELDNLSKHRRYEIRMSVYNAVGEGPPSPPQEVFVGEAVPTGAPQNVAVKAATATQLDVTWEPPPTESQNGDIQGYKIHFWEAQRQNESARVKTLFLPETGVKLKNLTGYTSYWVSIAAFNAAGDGPRSTPVTARTQQAAPSAPGSIRFSELTTTSVNVSWEPPPLPNGILEGYRLVYEPCMPVDGEGTAGASEGTRGGPGSASISAGVSKIVTVDVKGNSPLWMKVKDLAEGITYRFRIRAKTFAYGPDVEANITTGPGEGAPGPPGEPFISRYGSAITIHWTSGDPGQGPITRYVIEARPSDEGLWDILIKDIPKEVTSYTFSMDILKQGVSYDFRVIAVNDYGYGTPSTPSPSVSAQKANPFYEEWWFLVVIALVGLIFILLLVFVLIIRGQSKKYAKKSDSGNGSKANALTHGEMVSLDESSFPALELNNRRLSVKNSFCRKNGIYTRSPPRPSPGSLHYSDEDVTKYNDLIPAESSSLTEKPSEVSDSQGSDSEYEVDPAHQKAHSFVNHYISDPTYYNSWRRQQKGISRAQAYSYTESDSGEPDHTPLSNSTSTQQGSLFRPKASRTPTPQTPGNPPSQPGTLYRPPSSLAPGSRAPIAGFSSFV", "ECO_0000256", "SignalP" ] ] }, "readme": "Name\n - Chicken Protein Signal Peptide\n\nVersion\n - v-2.12.1\n\nModified on\n - 2024-06-03T22:38:19.443Z\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Luke Johnson [luke.johnson@email.gwu.edu], Urnisha Bhuiyan [sbhuiyan28@email.gwu.edu], Cyrus Au-Yeung [cyruschauyeung@gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu], Kate Warner [k.warner1@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 Chicken Protein Signal Peptide dataset contains Gallus gallus [taxid:9031] signal peptide information for the UniProtKB canonical accessions. The dataset contains protein information, signal peptide sequence, signal peptide length, signal peptide start and end position, cleaved protein sequence, eco ids and PMIDs. The dataset contains related files in the output subdomain that includes processed protein sequence files in fasta format viz. Signal peptide sequence, protein sequence after signal peptide is cleaved, and full protein sequences of the proteins that contain signal peptide. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen. \n\nDescription Domain\n Keywords\n - signal peptide\n - ptm processing\n - UniProtKB\n\n Pipeline Steps\n - Step-1: The script extracts the signal peptide information from the triplestore and maps 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: uniprot-proteome-gallus-gallus.nt\n URI: https:/data.glygen.org/ln2downloads/ebi/2026_06_13/uniprot-proteome-gallus-gallus.nt\n Name: uniprot-proteome-gallus-gallus.nt\n URI: https:/data.glygen.org/ln2downloads/ebi/2026_06_13/uniprot-proteome-gallus-gallus.nt\n Name: uniprot-proteome-gallus-gallus.nt\n URI: https:/data.glygen.org/ln2downloads/ebi/2026_06_13/uniprot-proteome-gallus-gallus.nt\n Name: uniprot-proteome-gallus-gallus.nt\n URI: https:/data.glygen.org/ln2downloads/ebi/2026_06_13/uniprot-proteome-gallus-gallus.nt\n Output Subdomain\n Name: chicken_protein_signalp_annotation.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/chicken_protein_signalp_annotation.csv\n Name: chicken_protein_signalp_peptidesequences.fasta\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/chicken_protein_signalp_peptidesequences.fasta\n Name: chicken_protein_signalp_cleavedsequences.fasta\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/chicken_protein_signalp_cleavedsequences.fasta\n Name: chicken_protein_signalp_fullsequences.fasta\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/chicken_protein_signalp_fullsequences.fasta\n Name: chicken_protein_signalp_annotation.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/chicken_protein_signalp_annotation.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\"\n Description: \"\"\n Unique Values: \"2807\"\n Name: chicken_protein_signalp_peptidesequences.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/chicken_protein_signalp_peptidesequences.stat.csv\n\nFields\n Name: \"sequence\"\n Description: \"Amino acid sequence\"\n Unique Values: \"4562\"\n Name: chicken_protein_signalp_cleavedsequences.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/chicken_protein_signalp_cleavedsequences.stat.csv\n\nFields\n Name: \"sequence\"\n Description: \"Amino acid sequence\"\n Unique Values: \"4562\"\n Name: chicken_protein_signalp_fullsequences.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/chicken_protein_signalp_fullsequences.stat.csv\n\nFields\n Name: \"sequence\"\n Description: \"Amino acid sequence\"\n Unique Values: \"4562\"", "downloadurl": "/ln2data/releases/data/v-2.12.1/reviewed/chicken_protein_signalp_annotation.csv" }