[BioC] reverse complement or no reverse complemnt on biomaRt / biomart.org

[Tefina Paloma]

James W. MacDonald <jmacdon at ...> writes:


> 
> The flanking sequence isn't reverse complemented in R, it is reported 
> exactly as it is received from the Biomart server.
> 
> I am a bit confused here as well; AFAICT, the sequence for the 5' flank 
> and UTR are identical from all sources (Ensembl, Biomart and biomaRt).
> 
> 5' flank:
> Ensembl
> 
> ccgccgccagcgcccccgccgcagcgcccgcggcccggctcctctcactt
> 
> Biomart
> 
> CCGCCGCCAGCGCCCCCGCCGCAGCGCCCGCGGCCCGGCTCCTCTCACTT
> 
> biomaRt
> 
> CCGCCGCCAGCGCCCCCGCCGCAGCGCCCGCGGCCCGGCTCCTCTCACTT
> 
> 5'UTR
> 
> Ensembl
> 
> CACCCCTGCCCCCGCCAGCGGACCGGTCCCCCACCCCCGGTCCTTCCACC
> 
> Biomart
> 
> CACCCCTGCCCCCGCCAGCGGACCGGTCCCCCACCCCCGGTCCTTCCACC
> 
> biomaRt
> 
> CACCCCTGCCCCCGCCAGCGGACCGGTCCCCCACCCCCGGTCCTTCCACC
> 
> Best,
> 
> Jim

Dear Jim,

Do you know if these sequences are sense or antisense?
If you export the sequence via biomart (via the webpage), you get the following:

>ENST00000280193 utr5:KNOWN_protein_coding
CGGGGAAGGGGAGGGAGGAGGGGGACGAGGGCTCTGGCGGGTTTGGAGGGGCTGAACATC
GCGGGGTGTTCTGGTGTCCCCCGCCCCGCCTCTCCAAAAAGCTACACCGACGCGGACCGC
GGCGGCGTCCTCCCTCGCCCTCGCTTCACCTCGCGGGCTCCGAATGCGGGGAGCTCGGAT
GTCCGGTTTCCTGTGAGGCTTTTACCTGACACCCGCCGCCTTTCCCCGGCACTGGCTGGG
AGGGCGCCCTGCAAAGTTGGGAACGCGGAGCCCCGGACCCGCTCCCGCCGCCTCCGGCTC
GCCCAGGGGGGGTCGCCGGGAGGAGCCCGGGGGAGAGGGACCAGGAGGGGCCCGCGGCCT
CGCAGGGGCGCCCGCGCCCCCACCCCTGCCCCCGCCAGCGGACCGGTCCCCCACCCCCGG
TCCTTCCACC

>5' Flanking sequence chromosome:GRCh37:4:177713896:177713945:1
AAGTGAGAGGAGCCGGGCCGCGGGCGCTGCGGCGGGGGCGCTGGCGGCGG

So, in contrast to the web-view, the flanking sequence is reverse complemented.
Basically it is just a problem of correct definition and assignment.
So which sequences are sense and which are antisense.

Best,
Tefina