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

[James W. MacDonald]

Tefina Paloma wrote:
> Hi,
> 
> 
> So, regardless if the gene is on the forward or on the reverse strand, the
> "start coordinates" for any kind of sequence are always lower than the "end
> coordinates".
> e.g. for Gene ENSG00000150630, Transcript ENST00000280193 and Exon
> ENSE00001153189
> Start: 177,713,319  	
> End: 177,713,895
> 
> So, if the gene is on the reverse strand, the sequence actually goes from the
> "end coordinates" to the "start coordinates".
> 
> Am I right?

Yes. For instance, the six exons for VEGFC have the following coordinates:

EXON CHRO STRAND  START    END
1     4   -  177713319 177713895
2     4   -  177650687 177650900
3     4   -  177648932 177649122
4     4   -  177632653 177632804
5     4   -  177608975 177609081
6     4   -  177608341 177608674

Since we are on the reverse strand, the coordinates for each exon are to 
the left of the preceding exon (assuming conventional orientation of the 
chromosome, a la UCSC genome browser). Since the gene transcription 
moves from right to left for this gene, by definition the end coordinate 
of an exon is really the start of the sequence for that exon, and the 
start coordinate is really the end of the sequence for that exon.

In other words, base coordinates are always counted on the forward 
strand, regardless of the strand the gene is on.

Best,

Jim


> 
> Thanks a lot for all your help,
> 
> Tefina
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826