Question: Chromosome Strand
0
gravatar for rocky.irengbam
7.0 years ago by
rocky.irengbam0 wrote:

I extracted 3'UTR sequences from UCSC table browser and it gave me the sequences with the headers

>hg19_refGene_NM_032291 range=chr1:67208779-67210768 5'pad=0 3'pad=0 strand=+ repeatMasking=none
>hg19_refGene_NM_032785 range=chr1:48998527-48999844 5'pad=0 3'pad=0 strand=- repeatMasking=none

etc. I just want to know what does this strand + and - means? If have to search for a motif then for this - strand , do I need to convert it into + strand? or does it simply mean that the gene is present on the reverse strand of the chromosome?

Rocky

utr • 1.9k views
ADD COMMENTlink modified 7.0 years ago by seidel7.0k • written 7.0 years ago by rocky.irengbam0

Please see UCSC FAQ "EST strand direction".

And if you have to search for a motif, I guess that everything depends on the software you're using.

ADD REPLYlink modified 7.0 years ago • written 7.0 years ago by PoGibas4.8k
0
gravatar for seidel
7.0 years ago by
seidel7.0k
United States
seidel7.0k wrote:

You should check the sequence explicitly, but it typically means that the gene is encoded on the reverse strand of the chromosome and the sequence you have is already good to go in terms of searching for a motif, i.e. it is the reverse complement of the sequence with coordinates: chr1:48998527-48999844.

ADD COMMENTlink written 7.0 years ago by seidel7.0k
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