Brassica rapa

Brassica rapa

About Brassica rapa

BrassicaInfo Ensembl databases for Brassica rapa are made possible through a joint effort by the Ensembl Genomes group and Rothamsted Research. The data are also browsable at BrassEnsembl.

Brassica rapa is a widely cultivated leaf and root vegetable. The genome was sequenced as a contribution to the Multinational Brassica Genome Sequencing Project and was published in August 2011 (Wang X, et. al. Nature 2011).

This Ensembl Genomes site was originally developed by Rothamsted Research (RRes), allowing people to access the Brassica genome through the Ensembl user interface. From release 13 of Ensembl Genomes, the EBI will be maintaining the genome browser for B. rapa in the context of Ensembl Plants.

More information and statistics

View karyotype Example region

Genome assembly: IVFCAASv1

More information and statistics

Download DNA sequence (FASTA)

Example gene tree

Comparative genomics

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

More about comparative analysis

Download alignments (EMF)

Example gene Example 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)

Update your old Ensembl IDs

Variation

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

Variant Effect Predictor

Gramene/Ensembl Genomes Annotation

Additional annotations generated by the Gramene/Ensembl Genomes projects include:
  • The standard set of Gramene analyses detailed here.

Additional features

Further annotations generated by RRes are displayed as additional tracks:
  • Arabidopsis coding sequences aligned using BLAT:
    • Alignment parameters: minmatch(2), minscore(30), min identity(80), maxGap(2), evalue threshold(1e-5).
    • Dataset: 33,410 Arabidopsis TAIR v9 coding sequences.
    • External links: AtEnsembl transcripts.
  • A 95k Brassica unigene set generated by JCVI aligned using BLAT:
    • Alignment parameters: default blat (minmatch(2), minscore(30), min identity(90), maxGap(2), evalue threshold(1e-20)).
    • Dataset: 94,558 Brassica unigenes.
  • A 135k Brassica unigene set generated by RRes aligned using BLAT:
    • Alignment parameters: default blat (minmatch(2), minscore(30), min identity(90), maxGap(2), evalue threshold(1e-20)).
    • Dataset: 135 201 Brassica unigenes.
  • B. rapa BAC end sequences aligned using Decypher tera-blastn:
    • Alignment parameters: match_score(1), mismatch_score(-3), open_penalty(-5), extend_penalty(-2), gapped_alignment(banded), query_filtered, max_score(10), max alignment number(10), evalue threshold(1e-50), word_size (9), query_increment(3), extension_threshold(20), percent identity(95).
    • Dataset: 196,837 B. rapa BAC end sequences obtained from GenBank 5-Aug-2010.
    • External links: GenBank.
  • B. rapa ESTs aligned using Decypher tera-blastn:
    • Alignment parameters: match_score(1), mismatch_score(-1), open_penalty(-1), extend_penalty(-2), gapped_alignment(banded), query_filtered, max_score(10), max alignment number(10), evalue threshold(1e-20), word_size(9), query_increment(3), extension_threshold(20), percent identity(90).
    • Dataset: 902,700 Brassica ESTs obtained from GenBank 13-Aug-2010.
    • External links: GenBank.
  • Image credit: School Division, Houghton Mifflin Company