{ "_id": "AT1G08465", "name": "YAB2", "description": "Plant-specific transcription factor YABBY family protein", "biotype": "protein_coding", "taxon_id": 3702, "system_name": "arabidopsis_thaliana", "db_type": "core", "gene_idx": 989, "location": { "region": "1", "start": 2675813, "end": 2679824, "strand": 1, "map": "GCA_000001735.1" }, "xrefs": [ { "db": "Uniprot_gn", "ids": [ "YAB2" ] }, { "db": "UniParc", "ids": [ "UPI00000A2B9D" ] }, { "db": "Uniprot/SWISSPROT", "ids": [ "Q9XFB0" ] }, { "db": "STRING", "ids": [ "3702.AT1G08465.1" ] }, { "db": "RefSeq_peptide", "ids": [ "NP_001077490.1" ] }, { "db": "EMBL", "ids": [ "AF136539" ] }, { "db": "protein_id", "ids": [ "AEE28295.1", "AAF22893.1" ] }, { "db": "TAIR_TRANSLATION", "ids": [ "AT1G08465" ] }, { "db": "Uniprot/SPTREMBL", "ids": [ "A0A178WC90", "A0A178WCI8", "A0A178WE92" ] }, { "db": "RefSeq_dna", "ids": [ "NM_001084021.2" ] }, { "db": "TAIR_LOCUS_MODEL", "ids": [ "AT1G08465.1" ] }, { "db": "NASC_GENE_ID", "ids": [ "AT1G08465" ] }, { "db": "EntrezGene", "ids": [ "3766682" ] }, { "db": "ArrayExpress", "ids": [ "AT1G08465" ] }, { "db": "TAIR_LOCUS", "ids": [ "AT1G08465" ] }, { "db": "TAIR_SYMBOL", "ids": [ "YAB2" ] }, { "db": "UniGene", "ids": [ "At.11866" ] } ], "synonyms": [ "At1g08465", "T27G7.15" ], "gene_structure": { "exons": [ { "id": "AT1G08465.1.exon1", "start": 1, "end": 289 }, { "id": "AT1G08465.1.exon2", "start": 2291, "end": 2422 }, { "id": "AT1G08465.1.exon3", "start": 2508, "end": 2628 }, { "id": "AT1G08465.1.exon4", "start": 2742, "end": 2790 }, { "id": "AT1G08465.1.exon5", "start": 2867, "end": 2942 }, { "id": "AT1G08465.1.exon6", "start": 3463, "end": 4012 } ], "transcripts": [ { "exons": [ "AT1G08465.1.exon1", "AT1G08465.1.exon2", "AT1G08465.1.exon3", "AT1G08465.1.exon4", "AT1G08465.1.exon5", "AT1G08465.1.exon6" ], "length": 1217, "exon_junctions": [ 289, 421, 542, 591, 667 ], "cds": { "start": 221, "end": 775 }, "translation": { "id": "AT1G08465.1", "length": 184, "features": { "family": { "entries": [ { "name": "PF04690", "description": "YABBY", "db": "Pfam", "interpro": "IPR006780", "start": 6, "end": 160 }, { "name": "PTHR31675", "description": "FAMILY NOT NAMED", "db": "PANTHER", "interpro": "IPR006780", "start": 1, "end": 184 } ] }, "homologous_superfamily": { "entries": [ { "name": "1.10.30.10", "description": null, "db": "Gene3D", "interpro": "IPR036910", "start": 104, "end": 156 }, { "name": "SSF47095", "description": "HMG-box", "db": "SuperFamily", "interpro": "IPR036910", "start": 105, "end": 153 } ] } } }, "id": "AT1G08465.1" } ], "canonical_transcript": "AT1G08465.1" }, "annotations": { "domains": { "entries": [ { "id": "IPR006780", "name": "YABBY", "description": "YABBY protein" }, { "id": "IPR036910", "name": "HMG_box_dom_sf", "description": "High mobility group box domain superfamily" } ] }, "GO": { "entries": [ { "id": "GO:0007275", "name": "multicellular organism development", "namespace": "biological_process", "def": "The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).", "subset": [ "goslim_chembl", "goslim_plant" ], "evidence_code": "IEA" }, { "id": "GO:0003677", "name": "DNA binding", "namespace": "molecular_function", "def": "Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).", "subset": [ "goslim_agr", "goslim_aspergillus", "goslim_candida", "goslim_chembl", "goslim_generic", "goslim_mouse", "goslim_plant", "goslim_yeast", "gosubset_prok" ], "evidence_code": "IEA" }, { "id": "GO:0003700", "name": "DNA binding transcription factor activity", "namespace": "molecular_function", "def": "Interacting selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a gene in order to modulate transcription.", "subset": [ "goslim_agr", "goslim_chembl", "goslim_generic", "goslim_metagenomics", "goslim_mouse", "goslim_plant", "goslim_yeast", "gosubset_prok" ], "evidence_code": "ISS" }, { "id": "GO:0046872", "name": "metal ion binding", "namespace": "molecular_function", "def": "Interacting selectively and non-covalently with any metal ion.", "subset": [ "goslim_agr", "goslim_metagenomics", "gosubset_prok" ], "evidence_code": "IEA" }, { "id": "GO:0010158", "name": "abaxial cell fate specification", "namespace": "biological_process", "def": "The process in which a cell becomes capable of differentiating autonomously into an abaxial cell in an environment that is neutral with respect to the developmental pathway; upon specification, the cell fate can be reversed.", "subset": null, "evidence_code": "IDA" }, { "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. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.", "subset": [ "goslim_agr", "goslim_aspergillus", "goslim_candida", "goslim_chembl", "goslim_generic", "goslim_metagenomics", "goslim_mouse", "goslim_pir", "goslim_plant", "goslim_yeast" ], "evidence_code": "IEA" } ], "ancestors": [ 1708, 3674, 3676, 5488, 5575, 5622, 5623, 6355, 8150, 9889, 9987, 10468, 10556, 19219, 19222, 30154, 31323, 31326, 32501, 32502, 43167, 43169, 43226, 43227, 43229, 43231, 44424, 44464, 45165, 48856, 48869, 50789, 50794, 51171, 51252, 60255, 65007, 80090, 97159, 140110, 1901363, 1903506, 2000112, 2001141 ] }, "PO": { "entries": [ { "id": "PO:0000293", "name": "guard cell", "namespace": "plant_anatomy", "def": "One of a pair of cells flanking the stomatal pore.", "subset": [ "CL", "TraitNet" ], "evidence_code": "IEP" }, { "id": "PO:0000021", "name": "petal primordium", "namespace": "plant_anatomy", "def": "A phyllome primordium (PO:0025128) that develops from a petal anlagen (PO:0025484) and is committed to the development of a petal (PO:0009032).", "subset": null, "evidence_code": "IDA" }, { "id": "PO:0000015", "name": "cotyledon primordium", "namespace": "plant_anatomy", "def": "A phyllome primordium (PO:0025128) that develops from a cotyledon anlagen (PO:0025432) and is part of a vegetative shoot apex (PO:0025223) and is committed to the development of a cotyledon (PO:0020030).", "subset": null, "evidence_code": "IDA" }, { "id": "PO:0000019", "name": "gynoecium primordium", "namespace": "plant_anatomy", "def": "A floral structure primordium (PO:0025477) that is committed to the development of a gynoecium (PO:0009062).", "subset": null, "evidence_code": "IDA" } ], "ancestors": [ 37, 2000, 4013, 5679, 6035, 9002, 9006, 9007, 9008, 9011, 9013, 25004, 25007, 25029, 25127, 25128, 25131, 25165, 25222, 25223, 25477, 25496, 25497, 25606 ] }, "taxonomy": { "entries": [ { "_id": 3702, "name": "Arabidopsis thaliana" } ], "ancestors": [ 1, 2759, 3193, 3398, 3699, 3700, 3701, 33090, 35493, 58023, 58024, 71240, 71275, 78536, 91827, 91836, 131221, 131567, 980083, 1437183, 1437201 ] }, "familyRoot": { "entries": [ { "_id": 3398, "name": "Magnoliophyta" } ], "ancestors": [ 1, 2759, 3193, 33090, 35493, 58023, 58024, 78536, 131221, 131567 ] } }, "summary": "Member of the YABBY family of Arabidopsis proteins involved in the abaxial cell fate specification in lateral organs", "homology": { "gene_tree": { "id": "EPlGT00140000000739", "root_taxon_id": 3398, "root_taxon_name": "Magnoliophyta", "duplications": [ 3398, 4232 ] }, "homologous_genes": { "ortholog_one2one": [ "fgenesh2_kg.1__861__AT1G08465.1", "A4A49_23983", "TanjilG_24155", "Csa_6G426940", "PRUPE_6G147600", "TCM_041175", "BVRB_7g171330", "F775_28710", "ORGLA12G0165000", "AMTR_s00004p00165390" ], "ortholog_one2many": [ "GSBRNA2T00104691001", "Bo8g112450", "Bra018624", "Bo8g055830", "GSBRNA2T00047230001", "GSBRNA2T00122244001", "GSBRNA2T00100579001", "Bra031629", "Bo5g009010", "GSBRNA2T00156238001", "Bra030728", "GSBRNA2T00019352001", "PGSC0003DMG400002988", "Solyc11g071810.1", "PGSC0003DMG400005936", "Solyc06g073920.2", "PHAVU_011G100300g", "GLYMA_12G096000", "POPTR_0001s22180", "VIT_08s0032g01110", "MTR_4g050300", "MANES_08G035700", "POPTR_0016s06760", "B456_006G117800", "Tp57577_TGAC_v2_gene4635", "GLYMA_06G308900", "MTR_2g087740", "MANES_11G103500", "B456_001G127000", "Tp57577_TGAC_v2_gene4209", "GLYMA_13G311200", "VIT_06s0009g00880", "MANES_04G064600", "GLYMA_12G190500", "PHAVU_005G117600g", "Si023308m.g", "GSMUA_Achr4G22750_001", "OPUNC03G25290", "OBART07G03740", "KN539964.1_FG007", "Zm00001d013662", "HORVU5Hr1G007270", "OMERI12G13460", "OB03G35470", "TRIUR3_27402", "Si037789m.g", "BGIOSGA025186", "Dr11140", "GSMUA_Achr4G31310_001", "Si030811m.g", "OB12G26050", "GSMUA_Achr3G15060_001", "Os03g0650000", "TRIAE_CS42_5AS_TGACv1_393321_AA1271170", "TRIAE_CS42_5DL_TGACv1_433350_AA1410470", "Zm00001d013661", "Os12g0621100", "GSMUA_Achr6G31080_001", "OGLUM03G28370", "TRIUR3_18590", "TRIAE_CS42_5DS_TGACv1_457157_AA1483350", "BGIOSGA013223", "OMERI07G02330", "HORVU5Hr1G007260", "OPUNC12G17340", "SORBI_3001G152901", "KN538757.1_FG005", "BRADI4G01300", "LPERR03G22960", "GSMUA_Achr2G12850_001", "GSMUA_Achr3G25660_001", "OGLUM07G03110", "ONIVA07G02310", "Os07g0160100", "ORUFI03G28820", "SORBI_3008G176300", "Zm00001d018829", "Dr03478", "GSMUA_AchrUn_randomG19410_001", "OBART03G27740", "SORBI_3002G039400", "OGLUM12G20870", "OB07G12810", "ONIVA03G28660", "GSMUA_Achr8G04750_001", "Zm00001d041277", "ONIVA02G03100", "OPUNC07G03670", "BRADI1G57070", "HORVU5Hr1G092430", "BGIOSGA037817", "TRIAE_CS42_5BL_TGACv1_404477_AA1301190", "LPERR12G16270", "Zm00001d013663", "ORUFI12G21410", "GSMUA_Achr7G01330_001", "OBART12G19190", "TRIAE_CS42_5AL_TGACv1_374236_AA1194610", "GSMUA_Achr7G07830_001", "LPERR07G03250", "BRADI1G13570", "TRIAE_CS42_5BS_TGACv1_423385_AA1375620", "GSMUA_Achr3G30800_001", "ORUFI07G03450", "GSMUA_Achr8G26600_001", "Zm00001d031109", "Zm00001d033508" ], "within_species_paralog": [ "AT2G26580", "AT1G69180", "AT1G23420", "AT4G00180", "AT2G45190" ] } }, "bins": { "fixed_100": 504, "fixed_200": 1006, "fixed_500": 2513, "fixed_1000": 5026, "uniform_1Mb": 1311, "uniform_2Mb": 672, "uniform_5Mb": 284, "uniform_10Mb": 158 }, "species_idx": 1 }