Ensembl Plants: Paralogs
ensembl_plants_paralogsFind paralogues of a plant locus using Ensembl Compara, returning duplication type, taxonomy level, and percent identity to reveal evolutionary relationships.
Instructions
List the paralogues Ensembl Compara (plants) records for a plant locus (rest.ensembl.org /homology, type=paralogues; free, no key). Each row gives the paralogue's locus, its type — within_species_paralog, or other_paralog: Ensembl's 'ancient paralogues', inferred across a super tree, so the two genes can sit in different gene trees — the taxonomy_level of the duplication, perc_id/perc_pos and protein_id, closest first. gramene_homologs carries only within_species_paralog, so a gene can have paralogues here and none there. A paralogue list is not a family list: other_paralog can name a gene outside the family (AT2G23390, an acyl-CoA N-acyltransferase-like gene, is an other_paralog of the ARFs); test membership with interpro_domains. An empty list means Compara records no paralogue, not that the gene is single-copy (FLS2, AT5G46330, has none). found=false when Compara keeps no homology record for the gene at all (e.g. a non-coding gene); an id Ensembl does not know is a not-found error. total and counts_by_type count before limit; truncated=true when limit cut some off.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| limit | No | ||
| locus | Yes | e.g. AT1G19850 (Arabidopsis), Os04g0519700 (rice) | |
| 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 | False when Compara keeps no homology record for this gene at all (e.g. a non-coding gene); true otherwise, even with no paralogue | |
| locus | Yes | The locus asked about | |
| total | Yes | How many paralogues exist upstream for this query, all pages (pre-cap) (#123) | |
| organism | Yes | Canonical organism slug | |
| paralogs | Yes | Closest first (perc_id descending) | |
| returned | Yes | Rows in this payload (#123) | |
| truncated | Yes | True when limit cut paralogues off | |
| counts_by_type | Yes | Paralogues per type, counted before limit | |
| upstream_version | No | Ensembl release that produced THIS response, — always null today: this backend states no release on its responses; upstream_release(backend='ensembl_plants') reports the release its own endpoint calls current at query time, or why there is none. null means Ensembl did not state one — never that no release exists, and never inferred from a separate metadata call, which can describe a different release than the one that answered. |