About Oryza nivaraOryza nivara is a wild rice from India; one of rice species being used in the OMAP project. It belongs to the AA genome group. Breeders are interested in this organism because it exhibits resistance to grassy stunt virus. It is found in swampy areas, at edges of ponds and tanks, beside streams, in ditches, in or around rice fields. It usually grows in shallow water up to 0.3 m. seasonally dry; in open habitats. It has 12 chromosomes and a nuclear genome size of 448Mb (flow cytometry). This work was part of the Oryza Genome Evolution project funded by NSF Award #1026200 and in collaboration with Y. Hsing (Taiwan).
What can I find? Homologues, gene trees, and whole genome alignments across multiple species.
Download alignments (EMF)
|Oryza nivara : Leersia perrieri||LASTZ_NET | stats|
|Oryza nivara : Oryza barthii||LASTZ_NET | stats|
|Oryza nivara : Oryza brachyantha||LASTZ_NET | stats|
|Oryza nivara : Oryza glaberrima||LASTZ_NET | stats|
|Oryza nivara : Oryza glumaepatula||LASTZ_NET | stats|
|Oryza nivara : Oryza longistaminata||LASTZ_NET | stats|
|Oryza nivara : Oryza meridionalis||LASTZ_NET | stats|
|Oryza nivara : Oryza punctata||LASTZ_NET | stats|
|Oryza nivara : Oryza rufipogon||LASTZ_NET | stats|
|Oryza nivara : Oryza sativa Indica||LASTZ_NET | stats|
|Oryza nivara : Oryza sativa Japonica||LASTZ_NET | stats|
This species currently has no variation database. However you can process your own variants using the Variant Effect Predictor:
Gramene/Ensembl Genomes Annotation
Additional annotations generated by the Gramene project include:
- Gene phylogenetic trees with other Gramene species: see example.
- Lastz Whole Genome Alignment to Oryza sativa Japonica (IRGSP v1), see example.
- Ortholog based DAGchainer synteny detection against other AA genomes, see example.
- Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see example.
- Identification of various repeat features from MIPS and AGI repeat libraries.