Hi Tefina,
I have had a look at your query and the reason for the confusion is  
that the "coding_gene_flank" returns not just the 5'UTR in this case,  
but also the intronic sequence that separates the 5'UTR. The "5utr"  
returns just UTR and no intronic sequence if the UTR has multiple  
exons. So when you selected "coding_gene_flank" you got this sequence  
back:


Partial first exon of 5' UTR (Missing from your 1000 upstream  
selection is this: ATTATGGGATTCAGCTG)
CCTCTGAAAACCTGTAGCCCAATAATGGTTATTCCCCAGGAGCCGCGCGAAGCATGAGCT
AATTTTCAGTGAGCGCGGACTTTGGGGTAACGGTTCCAGCACAGCACATCCCTTTCTCCT
CTTTTCACTCATCGTCACCGCTACCTGAAAACCCTGGCCGGGTGCTGGGGCTTGAGGAGC
AGTTCCCACTTCCCAGTCTTTTTCACTTTTCACAGCTGCAAAGTTCAGGGAGTTGAACTG
CAGTGCTTTCAGTTCACTGCTCACTCTGCCACGATCAATCTCTGTTGTAAATTTTCCTCC
CAGAGCACGTGACGATGCACTTCTTGACTATATATCCCAACTGCAGCAGCGGAGTTGTCA
GAGCGCAGAGCCGGACAGAGCAGAAGAACCCTCTTGGACTGGACGATTTGGGAATTCAAA
ACTTGGGACAAACTGTCAGCCTTG


Intron
GTAAGTCAGCAAGGCTACACTTTGCTTTCAGAAACA
TTTGAAAGAGGGACATTTTTGCCAATTAATAGATGAATTTTTTTCCTTTATTTTCTTCCT
GCTTTTCTTTGTTCTAAGGAAACATTGTTTTGAATTTAAAATAGTTTGGTTTTGGAAACA
CAATGTAAACTTTGTTTCTGCTCAGTTAAAATACGTTTCCCAGTTTTAAAGATACTATTT
ACTGTATGCTCCTGTCTTACATTGATTTTTTTTTTAATCAAAGTAATACTGCTCACTACA
AACAGGACAAATGTGTACACTAAAAAAAAAAAAAAAAGTCCTTCTTACTTTTCCCAGTGA
ACCTTCCCGGGCTTCTCTCCCGTGCACTCCAAGCCCTCATAGCTCACTCTTGTCAGCTGT
TTGGCGAACCCTCTTATGCTATTTCTTTCATGCACTTTTAAGCTTTTTTGGTATTGCAGT
TCCACAAACCTCGTGCTCCCCCACCTCCCTGTGCCCAGGACCTGGGGGAGAGTTCTAACC
TGCGGCTTTTTCCCCAG


Second exon of 5' UTR
CCCCTGCTGTGGAGGCAGCCTCA

So if you want to get all the 5'UTR you will need to extend your  
upstream cut off limit.
I hope this explains the difference between "coding_gene_flank" and  
"5utr".
Kind regards,
Rhoda



On 25 Sep 2009, at 14:16, Tefina Paloma wrote:

> Dear list,
>
> I do have a question regarding getSequence and the difference  
> between the
> seqType "coding_gene_flank" and "5utr".
> As far as I understand, "coding_gene_flank"  should contain the 5utr.
>
> Looking at an example:
>
> library(biomaR)
> ensembl <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
>
> flanking_seq <- getSequence(id = c(23704), type = "entrezgene",  
> seqType =
> "coding_gene_flank", upstream = 1000, mart = ensembl)
> 5utr   <- getSequence(id = c(23704), type = "entrezgene", seqType =  
> "5utr",
> mart = ensembl)
>
> So flanking_seq contains a sequence which is 1000 bases long,
> 5utr contains 154 bases.
>
> But:
> The 5utr does not align perfectly with the flanking_seq (only 131  
> bases
> align), and further more,
> the alignment start at base 313 of the flanking_seq.
>
> I would assume that the 5utr is at the end of the flanking_seq and  
> not in
> the middle?!
> And, of course, that the flanking_seq contains entirely the 5utr.
> So, what am I missing here?
>
> Thanks a lot in advance for any hints!
>
> Tefina
>
>> sessionInfo()
> R version 2.9.2 (2009-08-24)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.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_1.2-0   XML_2.6-0
>
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>
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> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.


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