{ "_id": "scaffold_502313.1", "name": "PAD4", "description": "Phytoalexin deficient 4 [Source:UniProtKB/TrEMBL;Acc:D7LU62]", "biotype": "protein_coding", "taxon_id": 81972, "system_name": "arabidopsis_lyrata", "db_type": "core", "gene_idx": 18462, "location": { "region": "5", "start": 16072441, "end": 16075497, "strand": 1, "map": "GCA_000004255.1" }, "xrefs": [ { "db": "TAIR_SYMBOL", "ids": [ "PAD4" ] }, { "db": "protein_id", "ids": [ "EFH52402" ] }, { "db": "RefSeq_peptide_predicted", "ids": [ "XP_002876143" ] }, { "db": "UniParc", "ids": [ "UPI0001C6977B" ] }, { "db": "EMBL", "ids": [ "GL348717" ] }, { "db": "Uniprot/SPTREMBL", "ids": [ "D7LU62" ] }, { "db": "Reactome", "ids": [ "REACT_14797" ] }, { "db": "RefSeq_mRNA_predicted", "ids": [ "XM_002876097" ] }, { "db": "RefSeq_dna_predicted", "ids": [ "XM_002876097" ] }, { "db": "EntrezGene", "ids": [ "9312211" ] }, { "db": "WikiGene", "ids": [ "9312211" ] } ], "gene_structure": { "exons": [ { "id": "scaffold_502313.1.exon1", "start": 1, "end": 311 }, { "id": "scaffold_502313.1.exon2", "start": 1700, "end": 3057 } ], "transcripts": [ { "exons": [ "scaffold_502313.1.exon1", "scaffold_502313.1.exon2" ], "length": 1669, "exon_junctions": [ 311 ], "cds": { "start": 21, "end": 1649 }, "translation": { "id": "scaffold_502313.1", "length": 542, "features": { "domain": { "entries": [ { "name": "PF01764", "description": "Fungal lipase-like domain", "db": "Pfam", "interpro": "IPR002921", "start": 110, "end": 185 }, { "name": "3.40.50.1820", "description": "Alpha/Beta hydrolase fold", "db": "Gene3D", "interpro": "IPR029058", "start": 109, "end": 234 }, { "name": "SSF53474", "description": "Alpha/Beta hydrolase fold", "db": "Superfamily", "interpro": "IPR029058", "start": 110, "end": 200 } ], "architecture": [ { "root": "29058", "start": 109, "end": 234, "interpro": "IPR029058", "name": "AB_hydrolase", "description": "Alpha/Beta hydrolase fold" } ], "roots": "29058" } } }, "id": "scaffold_502313.1" } ], "canonical_transcript": "scaffold_502313.1" }, "annotations": { "domains": { "entries": [ { "id": "IPR002921", "name": "Fungal_lipase-like", "description": "Fungal lipase-like domain" } ], "ancestors": [ 29058 ] }, "GO": { "entries": [ { "id": "GO:0010618", "name": "aerenchyma formation", "namespace": "biological_process", "def": "The process that gives rise to aerenchyma, parenchyma tissue containing particularly large intercellular spaces of schizogenous or lysigenous origin. This process pertains to the initial formation of a structure from unspecified parts.", "subset": null }, { "id": "GO:0010942", "name": "positive regulation of cell death", "namespace": "biological_process", "def": "Any process that increases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.", "subset": null }, { "id": "GO:0009581", "name": "detection of external stimulus", "namespace": "biological_process", "def": "The series of events in which an external stimulus is received by a cell and converted into a molecular signal.", "subset": [ "gosubset_prok" ] }, { "id": "GO:0009816", "name": "defense response to bacterium, incompatible interaction", "namespace": "biological_process", "def": "A response of an organism to a bacterium that prevents the occurrence or spread of disease.", "subset": null }, { "id": "GO:0002213", "name": "defense response to insect", "namespace": "biological_process", "def": "A response to protect an organism from a directly detected or perceived external threat from an insect or insects to that organism.", "subset": null }, { "id": "GO:0004806", "name": "triglyceride lipase activity", "namespace": "molecular_function", "def": "Catalysis of the reaction: triacylglycerol + H2O = diacylglycerol + a carboxylate.", "subset": [ "goslim_chembl", "gosubset_prok" ] }, { "id": "GO:0001666", "name": "response to hypoxia", "namespace": "biological_process", "def": "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.", "subset": null }, { "id": "GO:0043900", "name": "regulation of multi-organism process", "namespace": "biological_process", "def": "Any process that modulates the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species.", "subset": [ "gosubset_prok" ] }, { "id": "GO:0010310", "name": "regulation of hydrogen peroxide metabolic process", "namespace": "biological_process", "def": "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving hydrogen peroxide.", "subset": null }, { "id": "GO:0009595", "name": "detection of biotic stimulus", "namespace": "biological_process", "def": "The series of events in which a biotic stimulus, one caused or produced by a living organism, is received and converted into a molecular signal.", "subset": [ "gosubset_prok" ] }, { "id": "GO:0030968", "name": "endoplasmic reticulum unfolded protein response", "namespace": "biological_process", "def": "The series of molecular signals generated as a consequence of the presence of unfolded proteins in the endoplasmic reticulum (ER) or other ER-related stress; results in changes in the regulation of transcription and translation.", "subset": null }, { "id": "GO:0009697", "name": "salicylic acid biosynthetic process", "namespace": "biological_process", "def": "The chemical reactions and pathways resulting in the formation of salicylic acid (2-hydroxybenzoic acid), a derivative of benzoic acid.", "subset": [ "gosubset_prok" ] }, { "id": "GO:0010150", "name": "leaf senescence", "namespace": "biological_process", "def": "The process that occurs in a leaf near the end of its active life that is associated with the dismantling of cell components and membranes, loss of functional chloroplasts, and an overall decline in metabolism.", "subset": null }, { "id": "GO:0035304", "name": "regulation of protein dephosphorylation", "namespace": "biological_process", "def": "Any process that modulates the frequency, rate or extent of removal of phosphate groups from a protein.", "subset": [ "gosubset_prok" ] }, { "id": "GO:0006629", "name": "lipid metabolic process", "namespace": "biological_process", "def": "The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.", "subset": [ "goslim_aspergillus", "goslim_candida", "goslim_chembl", "goslim_generic", "goslim_metagenomics", "goslim_pir", "goslim_plant", "goslim_pombe", "goslim_yeast", "gosubset_prok" ] }, { "id": "GO:0010200", "name": "response to chitin", "namespace": "biological_process", "def": "A process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chitin stimulus.", "subset": null }, { "id": "GO:0050832", "name": "defense response to fungus", "namespace": "biological_process", "def": "Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.", "subset": null }, { "id": "GO:0043069", "name": "negative regulation of programmed cell death", "namespace": "biological_process", "def": "Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes.", "subset": null }, { "id": "GO:0031348", "name": "negative regulation of defense response", "namespace": "biological_process", "def": "Any process that stops, prevents, or reduces the frequency, rate or extent of a defense response.", "subset": null }, { "id": "GO:0010363", "name": "regulation of plant-type hypersensitive response", "namespace": "biological_process", "def": "Any endogenous process that modulates the frequency, rate or extent of the plant hypersensitive response.", "subset": null }, { "id": "GO:0009867", "name": "jasmonic acid mediated signaling pathway", "namespace": "biological_process", "def": "A series of molecular signals mediated by jasmonic acid.", "subset": null }, { "id": "GO:0009862", "name": "systemic acquired resistance, salicylic acid mediated signaling pathway", "namespace": "biological_process", "def": "The series of molecular signals mediated by salicylic acid involved in systemic acquired resistance.", "subset": null }, { "id": "GO:0009738", "name": "abscisic acid-activated signaling pathway", "namespace": "biological_process", "def": "A series of molecular signals generated by the binding of the plant hormone abscisic acid (ABA) to a receptor, and ending with modulation of a cellular process, e.g. transcription.", "subset": null }, { "id": "GO:0009409", "name": "response to cold", "namespace": "biological_process", "def": "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cold stimulus, a temperature stimulus below the optimal temperature for that organism.", "subset": [ "gosubset_prok" ] }, { "id": "GO:0006612", "name": "protein targeting to membrane", "namespace": "biological_process", "def": "The process of directing proteins towards a membrane, usually using signals contained within the protein.", "subset": null }, { "id": "GO:0002679", "name": "respiratory burst involved in defense response", "namespace": "biological_process", "def": "A phase of elevated metabolic activity, during which oxygen consumption increases made as part of a defense response ; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals.", "subset": null }, { "id": "GO:0000165", "name": "MAPK cascade", "namespace": "biological_process", "def": "An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.", "subset": null }, { "id": "GO:0006355", "name": "regulation of transcription, DNA-templated", "namespace": "biological_process", "def": "Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.", "subset": [ "goslim_pombe", "gosubset_prok" ] }, { "id": "GO:0005634", "name": "nucleus", "namespace": "cellular_component", "def": "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. 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