GrameneOryza

An Ensembl-based genome browser, search interface, and FTP serving the 19K-RGP across all five references — with the stable Ensembl REST API for gene, region, variant-effect, and sequence queries.

Open GrameneOryza ↗ Jump to examples

README — what it is & what it hosts

The FTP holds the per-reference variant calls and their predicted effects; the browser visualizes them on the location, gene, and variation pages. Because GrameneOryza is built on Ensembl, the Ensembl REST API (rest.ensembl.org) gives documented, stable access for Oryza sativa.

Use this when… you need gene models, the predicted consequence of a variant (VEP), cross-reference coordinates, or to stream a VCF slice via a track hub / tabix.

Tutorial — the genome browser (OsMADS50)

From the location page, search OsMADS50 to reach its gene page.
Open the variation page and enable the 19K-RGP variation track.
Click a variant to inspect its predicted effect.

A video walkthrough is available at oryza.gramene.org/videotutorials.

Workflow — a locus' variants & effects via REST (no download)

Goal: for MADS14 (Os03g0752800), pull the gene model, all overlapping variants, and their predicted consequences. lookup/id → overlap/region (feature=variation) → vep → a tidy variant×consequence table. See Workflow A.

Examples

# Gene -> coordinates
curl -s "https://rest.ensembl.org/lookup/id/Os03g0752800?content-type=application/json"
# Variants overlapping the locus
curl -s "https://rest.ensembl.org/overlap/region/oryza_sativa/3:31031753-31041563?feature=variation;content-type=application/json"
# Predicted consequence (region/:-/)
curl -s "https://rest.ensembl.org/vep/oryza_sativa/region/3:31037240-31037240/A?content-type=application/json"

import oryza19k as o19
gene = o19.lookup_gene("Os03g0752800")                       # MADS14
vars = o19.region_features("3:31031753-31041563", feature="variation")
vep  = o19.vep_effects("3:31037240:A")                       # -> intron_variant

Access & cite

Review During peer review the rice resources are served from a staging instance with reviewer credentials provided to the editor; at publication they move to public, login-free production endpoints. The durable variant archive is the European Variation Archive (PRJEB105137).

Cite: Tello-Ruiz et al. (Gramene, NAR); the GrameneOryza database paper; the Ensembl REST API.