How convert reverse strain location to forward strain location?

Question

[khanhlpbao]

I'm researching for making coverage of SRY gene on male samples. However, from what I read the location of SRY gene on GrCH37 is chrY:2,654,896-2,655,723 (reverse strain). But from what I search the location of Yp11.2, the band that SRY gene located is chrY:3,000,000-11,600,000. I guess that the location of SRY gene is on the reverse strain but I don't know how to convert it to forward strain.

Answer 1

[Istvan Albert]

what are you trying to do? There should be no need to convert the coordinate systems, to get the sequence from the reverse strand we use the forward coordinates, then take the reverse complement of that.

the "reverse" coordinates are the same as the forward ones, just start/end are swapped as it is going backwards

[khanhlpbao]

From what I'm read, the SRY gene located on the Yp11.2 band of chromosome Y. However, when checking the location I found that the location listed in GeneCard is outside of the band. I'm not sure is this because the location on Genecard has the "(reverse strand)" behind so I want to know how to convert location of reverse strand to forward to check whether or not the SRY gene located on Yp11.2 band.

[Istvan Albert]

ok so if I understood you right the issue that you are bringing up is that the band is defined as starting at position 3,000,000 but the gene is at 2,654,896 thus why is SRY considered to be in the band.

While I am not working in this field to me this sounds like a simple convention, the band is not starting really at 3 million rather around there - thus the border is a little more fuzzy and you can just as well consider SRY being in the band.

In the vast majority of cases coordinates are always specified on the forward strand (even for features on the reverse)