Orientation Of Sequence On Minus Strand In Ucsc Genome Browser

Question

[user]

What is the UCSC genome browser convention for displaying sequences on minus strand? The coordinates are always ascending which for minus strand genes means they are running opposite to start to end of gene. For the genomic sequences that UCSC shows, what is the convention? If the gene is on minus strand and forward strand is ATGC, will it show the reverse complement in left to right order?

Answer 1

[Devon Ryan]

It shows 5'->3' of the + strand.

[user]

5' -> 3' of DNA or RNA?

[Devon Ryan]

The browser itself is of the genome, so DNA.

Answer 2

[microfuge]

Hi,

Regardless of the strand the coordinate end is always greater than coordinate start. You are right, for a negative stranded gene when you extract a sequnece it will show a reverse complement in left to right order.