Genes on negative strand?

Question

[christylynn002]

I'm getting a little bit confused about how/why the UCSC reports genes on the negative strand. I've noticed that while downloading gene sequences, I need to use the reverse complement of some of the sequences to get the correct ordering of exons with the correct splice sites denoted. This doesn't make sense to me. Does that mean the gene of interest is not on the positive strand since we need to take the reverse complement of the negative strand?

For example, if a DNA sequence is reported on the positive strand, I get something as below (intron lowercase and exon uppercase):

agATCGCTGAgt

This makes sense because the splice sites are denoted correctly (ag-gt)

However, if a sequence is reported in the negative strand I get a sequence that looks like such:

acAATTCCct

From this, I think I need to take the reverse complement to get me a sequence that is an accurate representation of the gene sequence (correct splice sites denoted).

agGGAATTgt

Is the positive strand in these negative strand reported genes worthless?

I've also noted that when downloading sequences using custom tracks, the sequences are always reported in the positive strand, but it appears that some sequences are in fact on the negative strand. Why is that?

Answer 1

[Istvan Albert]

There are many ways to download data from UCSC so you should probably specify what exactly did you use (what table is selected etc). Always getting the sequence from the positive strand can be very confusing but if you think about it the coordinates are also always relative to the positive strand. There is no coordinate system that would start at the beginning of the negative strand. For this reason tools that extract sequences based on coordinates will produce the positive strand unless we set additional options to reverse complement the data. I do agree with you though that when downloading genes the downloading process should warn users about this.