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Bulk download introns, exons, and UTR regions from Ensembl for gene prediction training set

Hi, I would like to download labeled FASTA sequences of introns, exons, 5' UTR regions, and 3' UTR regions from a nonredundant set of human genes.

Ensembl allows me to do this for an individual gene by going to a page on an individual transcript variant (https://www.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000139618;r=13:32889611-32973805;t=ENST00000544455) and clicking Download Sequence > FASTA.

Is there a way to automatically download a file like that for several thousand genes? I would like them all to be human (or at least mammalian) and protein-coding. Biomart seems to be down right now, and I'm willing to try to use the Perl, REST, or SQL APIs, but I have no experience with any of those, so some direction would be appreciated.

Ultimately I want a database of DNA sequences labeled as intron, exon, 5' UTR, or 3' UTR. If other databases (e.g. RefSeq) can provide it, that would be great too. Thanks!

sequence annotation intron exon ensembl
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updated by Brian Gudenas Brian Gudenas • written by Katherine Huang • Katherine Huang

1 answer

Check out the biomaRt R package, specifically the getSequence function which allows you to use a list of gene identifiers (Ensembl, or entrezgene) to retrieve sequences of interest by changing the seqType parameter (cdna, 3utr, 5utr, gene_exon, gene_intron, etc..)

library(biomaRt)
mart = useMart("ensembl", dataset = "hsapiens_gene_ensembl")

Ensembl_IDs = c(ENSG00000139618, ENSG00000128731)

seqs = biomaRt::getSequence(id = Ensembl_IDs, 
           type="ensembl_gene_id",
           seqType = "gene_exon", 
           mart = mart)
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written by Brian Gudenas Brian Gudenas

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