Dear list,

having a look at the vegfc gene (located on the reverse strand) on the
website of biomart and querying the 5utr and the flanking sequence yields
the following:

http://www.ensembl.org/Homo_sapiens/Transcript/Export?db=core;g=ENSG00000150630;output=fasta;r=4:177604691-177713895;strand=feature;t=ENST00000280193;param=utr5;genomic=5_flanking;_format=HTML

Doing the same in R, yields essentially the same with the only difference
that in the case of the flanking sequence the reverse complement is given:

library(biomaRt)
library(Biostrings)

ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")

vegfc_fs = getSequence(id = c("ENST00000280193"), type =
"ensembl_transcript_id",
                    seqType = "transcript_flank", upstream = 3000,
                    mart = ensembl)

vegfc_utr = getSequence(id = c("ENST00000280193"), type =
"ensembl_transcript_id",
                    seqType = "5utr",  mart = ensembl)


As the gene is located on the reverse strand, one would probably be
interested in the reverse complement of the sequence returned by
ensemble/biomart.

Although it's nice that the flanking sequence is already reverse
complemented in R, it should be somehow documented.

And the question arises, why does biomaRt only return the reverse complement
of the flanking sequence but not of the utr?

I would appreciate any hints!
Thanks a lot in advance,
Best,
Tefina

> sessionInfo()
R version 2.9.1 (2009-06-26)
i386-pc-mingw32

locale:
LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
Kingdom.1252;LC_MONETARY=English_United
Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] Biostrings_2.12.8 IRanges_1.2.3     biomaRt_2.0.0

loaded via a namespace (and not attached):
[1] Biobase_2.4.1 RCurl_0.98-1  XML_2.5-3

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