RSAT - retrieve EnsEMBL sequence

Returns upstream, downstream, intronic, exonic, UTR, transcript, mRNA, CDS or gene sequences for a list of genes from the EnsEMBL database.
Multi-genome queries are supported: automatic retrieval of sequences for all the orthologs of the query genes, at a given taxonomical level.

Program developed by with the help of

Remark: If you want to retrieve sequences from an organism that is not in the EnsEMBL database, you can use the retrieve-seq program instead


Query organism     EnsEMBL database version: 111

Single organism
Multiple organisms         Optional filters    Homology type     Taxon 
      (Can be time-consuming)

Gene, transcript or protein IDs 

Upload gene list from file

Type of sequence to retrieve Options for upstream or downstream sequence
Sequence type 
 Mask repeats (only valid for organisms with annotated repeats)
 Mask coding sequences
 Avoid redundant sequences due to alternative transcripts
Organism name in sequence fasta header 
 Sequence position     From    To 
Relative to feature 
Prevent overlap with neighbouring 
Output   

      MANUAL TUTORIAL