Ensembl resources are currently in reduced functionality mode. Please see our blog post for the latest information and our Twitter feed

EnsemblEnsembl Home

Synteny

Synteny is the conserved order of aligned genomic blocks between species. It is calculated from the pairwise genome alignments created by Ensembl, when both species have a chromosome-level assembly.

The search is run in two phases:

  1. We search for alignment blocks that are in the same order in the two genomes. Syntenic alignments that are closer than 200 kb are grouped into a synteny block.
  2. Groups that are in synteny are linked, provided that no more than two non-syntenic groups are found between them and they are less than 3 Mb apart.