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Oryza punctata (Oryza_punctata_v1.2) ▼

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About Oryza punctata

Oryza punctata is a wild rice species native to Africa. Breeders are interested because of demonstrated resistance to bacterial blight and brown plant hoppers. O. punctata, a diploid, belongs to the O. officinalis complex within the Oryzeae genome groups, and belongs to the BB genome type. It can be found in open or semi-open habitats such as forest margins, grassland and thickets, scrub lands, open bush or shifting cultivation fields, and rice fields. It has 12 chromosomes and a nuclear genome size of 423Mb (flow cytometry). This work was part of the OGE project funded by NSF Award #1026200.

Taxonomy ID 4537

Data source Oryza Genome Evolution Project

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View karyotypeExample region

Genome assembly: Oryza_punctata_v1.2

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Download DNA sequence (FASTA)

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Example geneExample transcript

Gene annotation

What can I find? Protein-coding and non-coding genes, splice variants, cDNA and protein sequences, non-coding RNAs.

More about this genebuild

Download genes, cDNAs, ncRNA, proteins - FASTA - GFF3

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Example gene tree

Comparative genomics

What can I find? Homologues, gene trees, and whole genome alignments across multiple species.

More about comparative analyses

Phylogenetic overview of gene families

Download alignments (EMF)

Variation

This species currently has no variation database. However you can process your own variants using the Variant Effect Predictor:

Regulation

What can I find? Microarray annotations.

More about the Ensembl Plants microarray annotation strategy

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.