JASPAR: TF Binding Motifs
tf_binding_motifsFetch curated transcription-factor DNA binding motifs for a plant locus from JASPAR. Resolves the locus to UniProt and gene symbol, returns confirmed motifs with IUPAC consensus, assay type, and sequence logo.
Instructions
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.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| locus | Yes | e.g. AT2G46830 (Arabidopsis CCA1), Os01g0100100 (rice RAP-DB) | |
| organism | No | Plant organism — accepts canonical slug (arabidopsis_thaliana), scientific or common name, or NCBI taxid | arabidopsis_thaliana |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| found | Yes | True if any profile was UniProt-confirmed for this locus | |
| locus | Yes | ||
| motifs | No | UniProt-confirmed binding profiles | |
| tax_id | Yes | NCBI taxid the JASPAR search was scoped to | |
| accession | Yes | Resolved UniProt accession | |
| truncated | Yes | True if the motif list was capped | |
| motif_count | Yes | Total confirmed profiles (pre-cap) | |
| name_only_matches | No | Name-similarity hits belonging to a DIFFERENT gene [{matrix_id, name, uniprot_ids}] — not this locus's motifs | |
| gene_names_searched | No | Gene symbols used as JASPAR search keys |