Sense/Antisense Gene Knockin Question

Question

[thorerges]

Hi All,

I am interested in knocking in a TagRFP in this gene in c. elegans. Sequence below is from Ensembl (http://useast.ensembl.org/Caenorhabditis_elegans/Gene/Sequence?db=core;g=WBGene00001946;r=III:12367474-12369050):

According to this, the gene is on the antisense strand. So, is the sequence displayed in ensembl the antisense sequence? Or is it the complementary sense sequence? How do I confirm?

This is important because my knock-in construct should be in the same direction as my gene, so that upon translation - the TagRFP actually fluoresces.

Thank you very much!

Answer 1

[Anima Mundi]

Hello,

Your gene has its sense strand in the reverse genomic strand. Ensembl Genome Browser displays invariably the forward genomic strand. The FASTA you attach shows the reverse genomic strand (-1, see also your FASTA header, or see the location field in the linked page). In any case, you can BLAT a given sequence in Ensembl to check whether it is found in the forward or in the reverse genomic strand.

[thorerges]

Sorry, does the sequence above correspond to the forward genomic strand or the reverse genomic strand? More specifically, does the ATG codon (highlighted in brown) correspond to the start codon of the gene in the 5'->3' direction?

[Anima Mundi]

No problem, the sequence above corresponds to the reverse genomic strand, which in this case implies that for you gene are visualised (5' to 3') first the start codon and then the stop codon. In other words, this is the strand you need!