Ensembl Plants Variation

Ensembl Genomes imports variations including Single Nucleotide Polymorphisms (SNPs) and insertion-deletion mutations (Indels) from various sources. Any effects on transcripts in the area are calculated.

Rice variations were obtained from NCBI dbSNP. Variations in Arabidopsis thaliana are largely from a BBSRC-funded collaboration between Richard Mott at the Wellcome Trust Centre for Human Genetics in Oxford and Paula Kover at the University of Bath, plus the results from screening Arabidopsis strains with the Affymetrix Arabidopsis SNP chip. Grape variations were determined from a collection of grape cultivars and wild Vitis species from the USDA germplasm collection.

Variations and sources can be viewed in the browser through pages such as:

  • Gene: Variation table and Variation image (for all variations in a gene)
  • Transcript: Population comparison and Comparison image (for all variations in a transcript across different sequences)
  • Location: Region in Detail (Variations can be drawn using "Configure this page" at the left). The menu allows display of information in Ensembl databases along with external sources in DAS format.

Variation Types

The variation types describe the location or effect on the transcript.

  • Non-synonymous SNPs - SNPs that are located in the coding sequence and result in an amino acid change in the encoded peptide sequence.
  • Synonymous SNPs - In coding sequence, not resulting in an amino acid change (i.e. silent mutation).
  • Frameshift variations - In coding sequence, resulting in a frameshift.
  • Stop lost - In coding sequence, resulting in the loss of a stop codon.
  • Stop gained - In coding sequence, resulting in the gain of a stop codon (i.e. leading to a shortened peptide sequence).
  • Essential splice site - In the first 2 or the last 2 basepairs of an intron.
  • Splice site - 1-3 bps into an exon or 3-8 bps into an intron.
  • Upstream variations - Within 5 kb upstream of the 5prime end of a transcript.
  • Regulatory region variations - In regulatory region annotated by Ensembl.
  • 5prime UTR variations - In 5prime UTR (untranslated region).
  • Intronic variations - In intron.
  • 3prime UTR variations - In 3prime UTR.
  • Downstream variations - Within 5 kb downstream of the 3prime end of a transcript.
  • Intergenic variations - More than 5 kb either upstream or downstream of a transcript.
  • Complex InDel - Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border.
  • Within mature miRNA - Located within a microRNA.
  • Within non-coding gene - Located within a gene that does not code for a protein.

Clicking on any variation on an Ensembl page will open a Variation tab with information about the flanking sequence and source for the selected variation. Links to genes and transcripts that include the variation can be found at the left of this tab.

Variation information can also be accessed using BioMart (gene database), and the Perl API (variation databases).