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Sequence and assembly

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Contigs

Track showing underlying assembly contigs.
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Track showing sequence in both directions. Only displayed at 1Kb and below.

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Genes and transcripts

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Genes (Genes (Ensembl))

This track comprises multiple analyses; Chloroplast protein-coding genes imported from Genbank.; Genes by The Rice Annotation Project (RAP) dated 2022-09-01.; Mitochondrial gene models imported from Genbank.
Rfam RNA Genes (Genes)

RNA genes produced by filtering alignments of Rfam (release 12.2) covariance models.
ncRNA Genes (Genes)

ncRNA genes annotated in ENA
tRNA Genes (Genes)

RNA genes produced by filtering predictions from tRNAscan-SE v1.23.
IRGSP Gene Prediction (IRGSP gene prediction)

Gene prediction by The Rice Annotation Project (RAP) dated 2017-08-04. Read more...
IRGSP nonCoding Genes (IRGSP nonCoding Gene Prediction)

NonCoding gene prediction by The Rice Annotation Project (RAP) dated 2017-08-04. Read more...
MSU Genes (MSU gene)

Gene annotation by MSU Rice Genome Annotation Project dated 2011-10-31. These genes are included alongside the IRGSP annotations, but are not included in Compara or BioMart. Read more...;

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FGENESH prediction

Ab initio prediction of protein coding genes, based on the genomic sequence alone AA Salamov et al., Genome Res. 2000 4:516-22.
MSU7 TE-related genes

TE-related Gene annotation by MSU through a process of automatic and manual curation

mRNA and protein alignments

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Comparative genomics

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Sequence variants (all sources) (Variant - All sources)

Sequence variants from all sources

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Smaller structural variants (all sources) (SV - Smaller variants)

Structural variants from all sources which are less than 1Mb in length. The colours correspond to the structural variant classes.
For an explanation of the display, see the dbVar documentation.

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