These are Araport services that can parse Araport11 GFF3 files, extract information (including features), and convert them into a JSON format.
Given a valid AGI locus return it's features from the Araport11 Release (06/2016) annotation in JSON format consumable by the jBrowse genome browser. This service uses ThaleMine to retrieve chromosome location information and the araport11_genomic_region_to_jbrowse service to extract the features.
$ http "https://api.araport.org/community/v0.3/araport/araport11_gene_structure_by_locus_v1.1/search?locus=AT1G65480" Authorization:"Bearer $TOKEN"
{
"features": [
{
"description": "PEBP (phosphatidylethanolamine-binding protein) family protein",
"end": 24333999,
"name": "AT1G65480",
"score": 0,
"start": 24331373,
"strand": 1,
"subfeatures": [
{
"end": 24333999,
"name": "AT1G65480.2",
"score": 0,
"start": 24331373,
"strand": 1,
"subfeatures": [
{
"end": 24331710,
"name": "FT:exon:1",
"score": 0,
"start": 24331373,
"strand": 1,
"type": "exon",
"uniqueID": "AT1G65480:exon:1"
},
{
"end": 24331377,
"name": "FT:five_prime_UTR:1",
"score": 0,
"start": 24331373,
"strand": 1,
"type": "five_prime_UTR",
"uniqueID": "AT1G65480:five_prime_UTR:1"
},
{
"end": 24331710,
"name": "FT:CDS:1",
"phase": "0",
"score": 0,
"start": 24331378,
"strand": 1,
"type": "CDS",
"uniqueID": "AT1G65480:CDS:1"
},
{
"end": 24332587,
"name": "FT:CDS:3",
"phase": "0",
"score": 0,
"start": 24332526,
"strand": 1,
"type": "CDS",
"uniqueID": "AT1G65480:CDS:3"
},
{
"end": 24332587,
"name": "FT:exon:3",
"score": 0,
"start": 24332526,
"strand": 1,
"type": "exon",
"uniqueID": "AT1G65480:exon:3"
},
{
"end": 24333341,
"name": "FT:CDS:4",
"phase": "1",
"score": 0,
"start": 24333301,
"strand": 1,
"type": "CDS",
"uniqueID": "AT1G65480:CDS:4"
},
{
"end": 24333341,
"name": "FT:exon:4",
"score": 0,
"start": 24333301,
"strand": 1,
"type": "exon",
"uniqueID": "AT1G65480:exon:4"
},
{
"end": 24333689,
"name": "FT:CDS:5",
"phase": "2",
"score": 0,
"start": 24333466,
"strand": 1,
"type": "CDS",
"uniqueID": "AT1G65480:CDS:5"
},
{
"end": 24333999,
"name": "FT:exon:6",
"score": 0,
"start": 24333466,
"strand": 1,
"type": "exon",
"uniqueID": "AT1G65480:exon:6"
},
{
"end": 24333999,
"name": "FT:three_prime_UTR:2",
"score": 0,
"start": 24333690,
"strand": 1,
"type": "three_prime_UTR",
"uniqueID": "AT1G65480:three_prime_UTR:2"
}
],
"type": "mRNA",
"uniqueID": "AT1G65480.2"
},
{
"end": 24333935,
"name": "AT1G65480.1",
"score": 0,
"start": 24331428,
"strand": 1,
"subfeatures": [
{
"end": 24331710,
"name": "FT:exon:2",
"score": 0,
"start": 24331428,
"strand": 1,
"type": "exon",
"uniqueID": "AT1G65480:exon:2"
},
{
"end": 24331509,
"name": "FT:five_prime_UTR:2",
"score": 0,
"start": 24331428,
"strand": 1,
"type": "five_prime_UTR",
"uniqueID": "AT1G65480:five_prime_UTR:2"
},
{
"end": 24331710,
"name": "FT:CDS:2",
"phase": "0",
"score": 0,
"start": 24331510,
"strand": 1,
"type": "CDS",
"uniqueID": "AT1G65480:CDS:2"
},
{
"end": 24332587,
"name": "FT:CDS:3",
"phase": "0",
"score": 0,
"start": 24332526,
"strand": 1,
"type": "CDS",
"uniqueID": "AT1G65480:CDS:3.1"
},
{
"end": 24333341,
"name": "FT:CDS:4",
"phase": "1",
"score": 0,
"start": 24333301,
"strand": 1,
"type": "CDS",
"uniqueID": "AT1G65480:CDS:4.1"
},
{
"end": 24333689,
"name": "FT:CDS:5",
"phase": "2",
"score": 0,
"start": 24333466,
"strand": 1,
"type": "CDS",
"uniqueID": "AT1G65480:CDS:5.1"
},
{
"end": 24333935,
"name": "FT:exon:5",
"score": 0,
"start": 24333466,
"strand": 1,
"type": "exon",
"uniqueID": "AT1G65480:exon:5"
},
{
"end": 24333935,
"name": "FT:three_prime_UTR:1",
"score": 0,
"start": 24333690,
"strand": 1,
"type": "three_prime_UTR",
"uniqueID": "AT1G65480:three_prime_UTR:1"
}
],
"type": "mRNA",
"uniqueID": "AT1G65480.1"
}
],
"type": "gene",
"uniqueID": "AT1G65480"
}
]
}
Given a desired chromosomal region, query the ThaleMine JBrowse REST API endpoint, extract features, and return data in JBrowse compatible JSON format.
$ http "https://api.araport.org/community/v0.3/araport/araport11_genomic_region_to_jbrowse_v0.1/search?q=features&chr=Chr1&start=216843&end=225822&featuretype=mRNA&level=1" Authorization:"Bearer $TOKEN"
{
"features": [
{
"description": "ferric reduction oxidase 1",
"end": 217734,
"name": "AT1G01590.1",
"score": 0,
"start": 214150,
"strand": 1,
"subfeatures": [
{
"end": 214406,
"name": "FRO1:exon:1",
"score": 0,
"start": 214150,
"strand": 1,
"type": "exon",
"uniqueID": "AT1G01590:exon:1"
},
{
"end": 214228,
"name": "FRO1:five_prime_UTR:1",
"score": 0,
"start": 214150,
"strand": 1,
"type": "five_prime_UTR",
"uniqueID": "AT1G01590:five_prime_UTR:1"
},
{
"end": 214406,
"name": "FRO1:CDS:1",
"phase": "0",
"score": 0,
"start": 214229,
"strand": 1,
"type": "CDS",
"uniqueID": "AT1G01590:CDS:1"
},
{
"end": 214582,
"name": "FRO1:CDS:2",
"phase": "2",
"score": 0,
"start": 214480,
"strand": 1,
"type": "CDS",
"uniqueID": "AT1G01590:CDS:2"
},
{
"end": 214582,
"name": "FRO1:exon:2",
"score": 0,
"start": 214480,
"strand": 1,
"type": "exon",
"uniqueID": "AT1G01590:exon:2"
},
{
"end": 214897,
"name": "FRO1:CDS:3",
"phase": "1",
"score": 0,
"start": 214697,
"strand": 1,
"type": "CDS",
"uniqueID": "AT1G01590:CDS:3"
},
{
"end": 214897,
"name": "FRO1:exon:3",
"score": 0,
"start": 214697,
"strand": 1,
"type": "exon",
"uniqueID": "AT1G01590:exon:3"
},
{
"end": 215554,
"name": "FRO1:CDS:4",
"phase": "1",
"score": 0,
"start": 215317,
"strand": 1,
"type": "CDS",
"uniqueID": "AT1G01590:CDS:4"
},
{
"end": 215554,
"name": "FRO1:exon:4",
"score": 0,
"start": 215317,
"strand": 1,
"type": "exon",
"uniqueID": "AT1G01590:exon:4"
},
{
"end": 215960,
"name": "FRO1:CDS:5",
"phase": "0",
"score": 0,
"start": 215633,
"strand": 1,
"type": "CDS",
"uniqueID": "AT1G01590:CDS:5"
},
{
"end": 215960,
"name": "FRO1:exon:5",
"score": 0,
"start": 215633,
"strand": 1,
"type": "exon",
"uniqueID": "AT1G01590:exon:5"
},
{
"end": 216293,
"name": "FRO1:CDS:6",
"phase": "2",
"score": 0,
"start": 216044,
"strand": 1,
"type": "CDS",
"uniqueID": "AT1G01590:CDS:6"
},
{
"end": 216293,
"name": "FRO1:exon:6",
"score": 0,
"start": 216044,
"strand": 1,
"type": "exon",
"uniqueID": "AT1G01590:exon:6"
},
{
"end": 217090,
"name": "FRO1:CDS:7",
"phase": "1",
"score": 0,
"start": 216414,
"strand": 1,
"type": "CDS",
"uniqueID": "AT1G01590:CDS:7"
},
{
"end": 217090,
"name": "FRO1:exon:7",
"score": 0,
"start": 216414,
"strand": 1,
"type": "exon",
"uniqueID": "AT1G01590:exon:7"
},
{
"end": 217304,
"name": "FRO1:CDS:8",
"phase": "2",
"score": 0,
"start": 217165,
"strand": 1,
"type": "CDS",
"uniqueID": "AT1G01590:CDS:8"
},
{
"end": 217734,
"name": "FRO1:exon:8",
"score": 0,
"start": 217165,
"strand": 1,
"type": "exon",
"uniqueID": "AT1G01590:exon:8"
},
{
"end": 217734,
"name": "FRO1:three_prime_UTR:1",
"score": 0,
"start": 217305,
"strand": 1,
"type": "three_prime_UTR",
"uniqueID": "AT1G01590:three_prime_UTR:1"
}
],
"type": "mRNA",
"uniqueID": "AT1G01590.1"
},
{
"description": "cytochrome P450%2C family 86%2C subfamily A%2C polypeptide 4",
"end": 221286,
"name": "AT1G01600.1",
"score": 0,
"start": 218834,
"strand": 1,
"subfeatures": [
{
"end": 219621,
"name": "CYP86A4:exon:1",
"score": 0,
"start": 218834,
"strand": 1,
"type": "exon",
"uniqueID": "AT1G01600:exon:1"
},
{
"end": 219199,
"name": "CYP86A4:five_prime_UTR:1",
"score": 0,
"start": 218834,
"strand": 1,
"type": "five_prime_UTR",
"uniqueID": "AT1G01600:five_prime_UTR:1"
},
{
"end": 219621,
"name": "CYP86A4:CDS:1",
"phase": "0",
"score": 0,
"start": 219200,
"strand": 1,
"type": "CDS",
"uniqueID": "AT1G01600:CDS:1"
},
{
"end": 220994,
"name": "CYP86A4:CDS:2",
"phase": "1",
"score": 0,
"start": 219752,
"strand": 1,
"type": "CDS",
"uniqueID": "AT1G01600:CDS:2"
},
{
"end": 221286,
"name": "CYP86A4:exon:2",
"score": 0,
"start": 219752,
"strand": 1,
"type": "exon",
"uniqueID": "AT1G01600:exon:2"
},
{
"end": 221286,
"name": "CYP86A4:three_prime_UTR:1",
"score": 0,
"start": 220995,
"strand": 1,
"type": "three_prime_UTR",
"uniqueID": "AT1G01600:three_prime_UTR:1"
}
],
"type": "mRNA",
"uniqueID": "AT1G01600.1"
},
{
"description": "glycerol-3-phosphate acyltransferase 4",
"end": 224351,
"name": "AT1G01610.1",
"score": 0,
"start": 221642,
"strand": -1,
"subfeatures": [
{
"end": 222359,
"name": "GPAT4:exon:4",
"score": 0,
"start": 221642,
"strand": -1,
"type": "exon",
"uniqueID": "AT1G01610:exon:4"
},
{
"end": 221949,
"name": "GPAT4:three_prime_UTR:1",
"score": 0,
"start": 221642,
"strand": -1,
"type": "three_prime_UTR",
"uniqueID": "AT1G01610:three_prime_UTR:1"
},
{
"end": 222359,
"name": "GPAT4:CDS:4",
"phase": "2",
"score": 0,
"start": 221950,
"strand": -1,
"type": "CDS",
"uniqueID": "AT1G01610:CDS:4"
},
{
"end": 223096,
"name": "GPAT4:CDS:3",
"phase": "0",
"score": 0,
"start": 222622,
"strand": -1,
"type": "CDS",
"uniqueID": "AT1G01610:CDS:3"
},
{
"end": 223096,
"name": "GPAT4:exon:3",
"score": 0,
"start": 222622,
"strand": -1,
"type": "exon",
"uniqueID": "AT1G01610:exon:3"
},
{
"end": 223866,
"name": "GPAT4:CDS:2",
"phase": "1",
"score": 0,
"start": 223551,
"strand": -1,
"type": "CDS",
"uniqueID": "AT1G01610:CDS:2"
},
{
"end": 223866,
"name": "GPAT4:exon:2",
"score": 0,
"start": 223551,
"strand": -1,
"type": "exon",
"uniqueID": "AT1G01610:exon:2"
},
{
"end": 224255,
"name": "GPAT4:CDS:1",
"phase": "0",
"score": 0,
"start": 223945,
"strand": -1,
"type": "CDS",
"uniqueID": "AT1G01610:CDS:1"
},
{
"end": 224351,
"name": "GPAT4:exon:1",
"score": 0,
"start": 223945,
"strand": -1,
"type": "exon",
"uniqueID": "AT1G01610:exon:1"
},
{
"end": 224351,
"name": "GPAT4:five_prime_UTR:1",
"score": 0,
"start": 224256,
"strand": -1,
"type": "five_prime_UTR",
"uniqueID": "AT1G01610:five_prime_UTR:1"
}
],
"type": "mRNA",
"uniqueID": "AT1G01610.1"
},
{
"description": "plasma membrane intrinsic protein 1C",
"end": 227302,
"name": "AT1G01620.2",
"score": 0,
"start": 225665,
"strand": -1,
"subfeatures": [
{
"end": 226081,
"name": "PIP1C:exon:6",
"score": 0,
"start": 225665,
"strand": -1,
"type": "exon",
"uniqueID": "AT1G01620:exon:6"
},
{
"end": 225985,
"name": "PIP1C:three_prime_UTR:1",
"score": 0,
"start": 225665,
"strand": -1,
"type": "three_prime_UTR",
"uniqueID": "AT1G01620:three_prime_UTR:1"
},
{
"end": 226081,
"name": "PIP1C:CDS:5",
"phase": "0",
"score": 0,
"start": 225986,
"strand": -1,
"type": "CDS",
"uniqueID": "AT1G01620:CDS:5"
},
{
"end": 226311,
"name": "PIP1C:CDS:4",
"phase": "0",
"score": 0,
"start": 226171,
"strand": -1,
"type": "CDS",
"uniqueID": "AT1G01620:CDS:4"
},
{
"end": 226311,
"name": "PIP1C:exon:5",
"score": 0,
"start": 226171,
"strand": -1,
"type": "exon",
"uniqueID": "AT1G01620:exon:5"
},
{
"end": 226691,
"name": "PIP1C:CDS:3",
"phase": "2",
"score": 0,
"start": 226396,
"strand": -1,
"type": "CDS",
"uniqueID": "AT1G01620:CDS:3"
},
{
"end": 226691,
"name": "PIP1C:exon:4",
"score": 0,
"start": 226396,
"strand": -1,
"type": "exon",
"uniqueID": "AT1G01620:exon:4"
},
{
"end": 226960,
"name": "PIP1C:CDS:2",
"phase": "0",
"score": 0,
"start": 226849,
"strand": -1,
"type": "CDS",
"uniqueID": "AT1G01620:CDS:2"
},
{
"end": 227049,
"name": "PIP1C:exon:3",
"score": 0,
"start": 226849,
"strand": -1,
"type": "exon",
"uniqueID": "AT1G01620:exon:3"
},
{
"end": 227049,
"name": "PIP1C:five_prime_UTR:3",
"score": 0,
"start": 226961,
"strand": -1,
"type": "five_prime_UTR",
"uniqueID": "AT1G01620:five_prime_UTR:3"
},
{
"end": 227302,
"name": "PIP1C:exon:1",
"score": 0,
"start": 227079,
"strand": -1,
"type": "exon",
"uniqueID": "AT1G01620:exon:1"
},
{
"end": 227302,
"name": "PIP1C:five_prime_UTR:2",
"score": 0,
"start": 227079,
"strand": -1,
"type": "five_prime_UTR",
"uniqueID": "AT1G01620:five_prime_UTR:2"
}
],
"type": "mRNA",
"uniqueID": "AT1G01620.2"
},
{
"description": "plasma membrane intrinsic protein 1C",
"end": 227543,
"name": "AT1G01620.1",
"score": 0,
"start": 225665,
"strand": -1,
"subfeatures": [
{
"end": 226081,
"name": "PIP1C:CDS:5",
"phase": "0",
"score": 0,
"start": 225986,
"strand": -1,
"type": "CDS",
"uniqueID": "AT1G01620:CDS:5.1"
},
{
"end": 226311,
"name": "PIP1C:CDS:4",
"phase": "0",
"score": 0,
"start": 226171,
"strand": -1,
"type": "CDS",
"uniqueID": "AT1G01620:CDS:4.1"
},
{
"end": 226691,
"name": "PIP1C:CDS:3",
"phase": "2",
"score": 0,
"start": 226396,
"strand": -1,
"type": "CDS",
"uniqueID": "AT1G01620:CDS:3.1"
},
{
"end": 227176,
"name": "PIP1C:CDS:1",
"phase": "0",
"score": 0,
"start": 226849,
"strand": -1,
"type": "CDS",
"uniqueID": "AT1G01620:CDS:1"
},
{
"end": 227543,
"name": "PIP1C:exon:2",
"score": 0,
"start": 226849,
"strand": -1,
"type": "exon",
"uniqueID": "AT1G01620:exon:2"
},
{
"end": 227543,
"name": "PIP1C:five_prime_UTR:1",
"score": 0,
"start": 227177,
"strand": -1,
"type": "five_prime_UTR",
"uniqueID": "AT1G01620:five_prime_UTR:1"
}
],
"type": "mRNA",
"uniqueID": "AT1G01620.1"
}
]
}