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

Question

[Katherine Huang]

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!

Answer 1

[Brian Gudenas]

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)