Question: Orientation Of Sequence On Minus Strand In Ucsc Genome Browser
0
gravatar for user
6.0 years ago by
user790
United States
user790 wrote:

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?

ADD COMMENTlink modified 6.0 years ago by microfuge1.1k • written 6.0 years ago by user790
1
gravatar for Devon Ryan
6.0 years ago by
Devon Ryan90k
Freiburg, Germany
Devon Ryan90k wrote:

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

ADD COMMENTlink written 6.0 years ago by Devon Ryan90k

5' -> 3' of DNA or RNA?

ADD REPLYlink written 6.0 years ago by user790

The browser itself is of the genome, so DNA.

ADD REPLYlink written 6.0 years ago by Devon Ryan90k
0
gravatar for microfuge
6.0 years ago by
microfuge1.1k
microfuge1.1k wrote:

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.

ADD COMMENTlink written 6.0 years ago by microfuge1.1k
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