Plant Genomics

Resolve a locus to its OrthoDB ortholog group and cross-species member genes (data.orthodb.org; free, no key). Searches at the Viridiplantae level, then returns the group metadata (name, evolutionary rate) and member genes grouped by organism (organism, gene id, description). organism_count is the true cluster total; the member list is capped with truncated flagged. found=false when the locus maps to no ortholog group. Works for all 12 organisms. NOTE: unlike the other locus tools, organism= does NOT scope the search — the group is resolved from the locus id alone at the Viridiplantae level, and organism is only validated and echoed back. Passing a mismatched organism therefore still returns the locus's real group.

Fetch the PANTHER protein-family classification for a locus (pantherdb.org; free, no key). Returns the PANTHER family and subfamily (id + name) plus curated GO terms grouped by aspect (molecular_function / biological_process / cellular_component), the PANTHER protein class, and pathways. found=false when PANTHER cannot classify the locus. Complements the sequence-homology tools (gramene_homologs / consensus_homologs) with an evolutionary-family view. Works for all 12 organisms. Defaults to arabidopsis_thaliana; pass organism= for other species.

Fetch a gene record from Phytozome BioMart (phytozome-next.jgi.doe.gov). Defaults to arabidopsis_thaliana; pass organism= for other Phytozome proteomes (slug, scientific/common name, or NCBI taxid — e.g. glycine_max, sorghum_bicolor). Locus is the source-genome gene name (e.g. AT1G01010, Glyma.01G000100). Returns organism_name, gene_name, chromosome, gene_start, gene_end, strand, description.

Fetch metabolic annotation for a locus from PlantCyc / the Plant Metabolic Network (pmn.plantcyc.org; free BioCyc web-services API, no key). Walks gene → enzyme → catalyzed reactions → PlantCyc pathways in the organism's PGDB, returning enzymes[] + reactions[] (id/name) + pathways[] (id/name) — the metabolic-pathway view KEGG and GO don't provide. A non-enzymatic gene (e.g. a transcription factor) returns found=false with empty lists, not an error. reaction_count / pathway_count report true totals even when the lists are capped. 11 organisms have a PGDB (arabidopsis, rice, maize, soybean, grape, poplar, tomato, barley, sorghum, medicago, brachypodium); wheat is not yet mapped. Defaults to arabidopsis_thaliana (AraCyc, the best-curated); pass organism= for other species.

Resolve a plant locus to its canonical UniProtKB record. Prefers reviewed (Swiss-Prot) entries; falls back to unreviewed (TrEMBL) when no curated record exists (common for non-Arabidopsis plants). organism accepts a canonical slug, scientific/common name, or NCBI taxid (default arabidopsis_thaliana; e.g. oryza_sativa, zea_mays). Returns primaryAccession, uniProtkbId, entryType, recommendedName, geneNames, organism, taxonId, sequenceLength, web_url. This is the protein-side entry point — pair with InterPro / AlphaFold / Reactome / structural-bio tools.

Fetch protein-protein interaction partners from STRING-DB (string-db.org). Accepts either a UniProt accession or a locus identifier — the latter is resolved via UniProt first. Defaults to arabidopsis_thaliana; pass organism= for other plant species (slug, scientific/common name, or NCBI taxid). Returns first-neighbor partners with the combined STRING score plus per-channel sub-scores (experimental, database, textmining, predicted).

Fetch the TAIR curator-vetted Arabidopsis locus summary. Served via BAR/ThaleMine (U Toronto, Global Core Biodata Resource 2023) since TAIR's free per-locus REST API is gated behind a paid Phoenix Bioinformatics subscription. Returns TAIR curator summary + Araport11 computational description + NCBI Gene ID + cross-DB aliases (RefSeq, UniProt, TIGR locus-model IDs). Arabidopsis only. Alias of bar_gene_summary.

Fetch curated transcription-factor DNA binding motifs for a locus from JASPAR (jaspar.elixir.no; free, no key) — the cis-regulatory view. Resolves the locus → UniProt accession + gene symbol, searches JASPAR by symbol scoped to the organism's taxid, then CONFIRMS each candidate by matching the accession against the profile's uniprot_ids. Returns per motif the JASPAR matrix id, TF class/family, assay type (SELEX / ChIP-seq / PBM / DAP-seq), an IUPAC consensus derived from the position-frequency matrix (e.g. CACGTG, the G-box/ABRE core), motif length, PubMed refs, and an SVG sequence-logo URL. IMPORTANT: JASPAR's name search is fuzzy, so name-similarity hits belonging to a DIFFERENT gene are returned separately in name_only_matches and must NOT be attributed to this locus; only `motifs` is UniProt-confirmed. found=false means the gene has no curated profile (not a TF, or its family is unprofiled for that species) — a normal outcome, not an error. Use jaspar_motif to retrieve the raw matrix for any matrix_id. Coverage is Arabidopsis-heavy (1236 profiles) and thin elsewhere (maize 131, soybean 91, wheat 58, tomato 51, rice 10; Brachypodium and sorghum have none). Defaults to arabidopsis_thaliana; pass organism= for other species.

Predict a variant's molecular consequences with Ensembl VEP (rest.ensembl.org; free, no key). Variant-first (not locus-first): supply an Ensembl region (chr:start-end:strand, e.g. '1:10000-10000:1') and an alternate allele (e.g. 'C'); returns the most-severe consequence plus one row per overlapping transcript (consequence terms, IMPACT, and SIFT/PolyPhen when the variant is coding-missense). found=false when Ensembl reports no overlapping feature. Works for all 12 organisms. Defaults to arabidopsis_thaliana; pass organism= for other species.