Dear list,

I am trying to retrieve 5' flanking sequences and 5' utr for several genes.
Doing this via biomart.org or, respectively, biomarRt yields different
results.

An example, I want to retrieve the 5' flanking sequences (3000 bases) plus
the 5' utr for the gene with the EntrezID 23704.

My R code:

library(biomaRt)
ensembl <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
myseq   <- getSequence(id = c(23704), type = "entrezgene", seqType =
"coding_gene_flank", upstream = 3154, mart = ensembl)

The length of the 5'utr for this gene is exactly is 154, so this query
should really yield 3000 upstream bases plus the 5'utr.

But, doing this via biomart.org, I get the following:
http://www.ensembl.org/Homo_sapiens/Gene/Export?db=core;g=ENSG00000152049;output=fasta;r=2:223916862-223920353;strand=feature;t=ENST00000281830;time=1253696359.47541;st=utr5;genomic=5_flanking;_format=HTML

The length of both sequences is 3154, but if you blast them, the do not
align perfectly.

What do I miss?
Can it be related to the fact that biomaRt is using the dataset
hsapiens_gene_ensembl, version NCBI35
and biomaRt.org is using the Homo Sapiens genes, GRCh37?

Thanks a lot,
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  tools_2.9.1   XML_2.5-3

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