RSA-tools : retrieve EnsEMBL sequence

RSA-tools - 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: 71

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 genemRNACDS
Prevent overlap with neighbouring

Output serverdisplayemail

MANUAL

TUTORIAL

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 genemRNACDS Prevent overlap with neighbouring