About Oryza nivara
Oryza 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 448 Mb (flow cytometry). This work was part of the Oryza Genome Evolution project funded by NSF Award #1026200 and in collaboration with Yue-Ie Hsing.
Taxonomy ID 4536
Data source Oryza Genome Evolution Project
What can I find? Homologues, gene trees, and whole genome alignments across multiple species.
Download alignments (EMF)
|Oryza nivara : Arabidopsis thaliana||LASTZ_NET | stats|
|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 glumipatula||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 Group||LASTZ_NET | stats|
|Oryza nivara : Oryza sativa Japonica Group||LASTZ_NET | stats|
|Oryza nivara : Vitis vinifera||LASTZ_NET | stats|
This species currently has no variation database. However you can process your own variants using the Variant Effect Predictor:
What can I find? Microarray annotations.
Gramene/Ensembl Genomes Annotation
Additional annotations generated by the Gramene and Ensembl Plants project include:
- Gene phylogenetic trees with other Gramene species.
- LastZ Whole Genome Alignment to Arabidopsis thaliana, Oryza sativa Japonica (IRGSP v1) and other Oryza AA genomes.
- Orthologue based DAGchainer synteny detection against other AA genomes.
- Mapping to the genome of multiple sequence-based feature sets using Gramene BLAT pipeline.
- Identification of various repeat features by programs such as RepeatMasker with MIPS and AGI repeat libraries, and Dust, TRF.